From ff0e7bd8fab6c6d42606dc24a09cfa199e8e80cf Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Fri, 25 Feb 2022 12:38:00 +0200 Subject: [PATCH 01/28] Delete .DS_Store --- .DS_Store | Bin 8196 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index f376dcac842103f3fccf38580d5ae45fe7e841ba..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8196 zcmeHMTWl0n7(U;&z)VNlX{~KtE?ul##0FXy3uu64w#0O&Hqa^x5c+vmNnHJho;}eiDCz^aLAL$aVZGgikKlj!28DpcK|a6P}~l}I2dB?S31H6Aj0Knoa9kj1s6e<93ReVM3ssEU7 z&X5oo)?o(149w2}pFSnbVkXOEhOghhTc+zZHT{f8N$H}+OC+gGDqC81Bz?>oPJ5bH zaFbfTkKc7@-my&3?sOb$rmbZTn#S;eTAgxiPcv;J?>n2iK_-X0OW9B0}(0 zU=?#BeB)YpmRn4TvVW>nW8L>?rz&tv$uUfRST|hz_2vWEE=tvXSf4u zg-fxvWgWXCZxku6?yO@KhHTPQW;H8YAY)^vWu?s%!aAFGEUUwDP0w`fLp`2x+~Ydl z(JWO@uj}N!l;2s8N&O3}Dn7>k9CvmP8hMvcmd}*eE?>2J{l-mOx2L8m)XFNQTB+$S zny#6#jILo*_l_OX+^k{irhT-R@@aeK6Q+@uDeh3Wo`5US=FRYm*Ns#G%6cp z)s;J+q?apPo0Yhv>T;K*WeiJ*T9hr4x>xQlim-(6QDvJ{iAK36>kJLibGt&Eh$bcV zd#Rs~-LARb{+wac@H~pvmC@)SF5ju^hAv4`Lt^l2|Lr#<)(I9g2w_LlMtl9H;OsPUB^~g4Z#DcX0+E;v;;Fukamy z!g*Z46n?`WxQr{}2_w@?-Z%a50&$fvn5e|$;GiusabqUe`%GSQ+cNoLIj8U4)%VoY z##XQ25Z|&bIrHY{yzE(gyq<(U?*y@Y!c7xO5S>WAZ21bMzKf`69G^QmrYDWMgp*F1 z;?}F~tFKo%+r;gfwe^Y$nh>(DeQ+&lBY|#X6X{Bb`$D(rVWnPOL^KzkTOUyrwUp+8 z&~D#B+Qr0pp-r`tmhl-W|1Zk^Ct=UA^Xw9l^(y-Zi-@RIMA8`6pb;(Djs#L@#V$OC z4je!lokY^VQLArS1cH;tl7pi6*1knA=ABNP9ktz2{1UN2`Bvfwt UK>+`89IpQs!u8+h-!vFvP From c0d750687c28cc812e36907e40b2e4fdf7f26cfc Mon Sep 17 00:00:00 2001 From: BournSupremacy Date: Mon, 7 Mar 2022 17:26:32 +0200 Subject: [PATCH 02/28] Gene coverage scripts updates --- bin/adjCdhit.pl | 47 +++++ bin/bam2cov | Bin 0 -> 28232 bytes bin/blastCluster.pl | 215 +++++++++++++++++++ bin/breakGCscaf.pl | 69 ++++++ bin/ccov | Bin 0 -> 96120 bytes bin/filterNovelgene.pl | 349 ++++++++++++++++++++++++++++++ bin/getTaxClass.pl | 172 +++++++++++++++ bin/getUnalnCtg.pl | 138 ++++++++++++ bin/hupan | 230 ++++++++++++++++++++ bin/hupanLSF | 249 ++++++++++++++++++++++ bin/hupanSLURM | 249 ++++++++++++++++++++++ bin/linearK.pl | 384 ++++++++++++++++++++++++++++++++++ bin/pav_plot.R | 94 +++++++++ bin/plotNovelSeq.R | 23 ++ bin/plotQual.R | 14 ++ bin/rmCtm.pl | 221 +++++++++++++++++++ lib/HUPANgeneCovSLURM.pm | 2 +- lib/HUPANmapSLURM.pm | 2 +- lib/HUPANpTpGSLURM.pm | 15 +- lib/HUPANrmHighSLURM.pm | 1 + lib/HUPANsimSeqSLURM.pm | 12 +- lib/originalHUPANpTpGSLURM.pm | 232 ++++++++++++++++++++ src/ccov/CCOV.cpp | 7 + 23 files changed, 2714 insertions(+), 11 deletions(-) create mode 100755 bin/adjCdhit.pl create mode 100755 bin/bam2cov create mode 100755 bin/blastCluster.pl create mode 100755 bin/breakGCscaf.pl create mode 100755 bin/ccov create mode 100755 bin/filterNovelgene.pl create mode 100755 bin/getTaxClass.pl create mode 100755 bin/getUnalnCtg.pl create mode 100755 bin/hupan create mode 100755 bin/hupanLSF create mode 100755 bin/hupanSLURM create mode 100755 bin/linearK.pl create mode 100755 bin/pav_plot.R create mode 100755 bin/plotNovelSeq.R create mode 100755 bin/plotQual.R create mode 100755 bin/rmCtm.pl create mode 100644 lib/originalHUPANpTpGSLURM.pm diff --git a/bin/adjCdhit.pl b/bin/adjCdhit.pl new file mode 100755 index 0000000..d64e124 --- /dev/null +++ b/bin/adjCdhit.pl @@ -0,0 +1,47 @@ +#!/usr/bin/perl +use strict; +use warnings; + +my $usage="$0 +"; + +die $usage if @ARGV!=5; + +my ($fa,$facls,$con,$outfa,$outcls)=@ARGV; +my %h; +open(IN,$con); +while(){ + chomp; + my ($a,$b)=split /\t/,$_; + $h{$b}=$a; +} +close IN; + +open(OUT,">$outfa"); +open(IN,$fa); +while(){ + if(/^>([0-9]+)/){ + print OUT ">",$h{$1},"\n"; + } + else{ + print OUT $_; + } +} +close IN; +close OUT; + +open(OUT,">$outcls"); +open(IN,$facls); +while(){ + if(/^>/){ + print OUT $_; + } + else{ + my ($a,$b)=split /\.\.\./,$_; + my($c,$d)=split /\>/,$a; + print OUT $c,$h{$d},$b; + } +} +close IN; + + diff --git 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z)aV$E+R2OiX$Q&mP&{bDz+=gSNC01-OYu^8CmvXZ3SNWSFBj<#(>lDklf z(c}SOquojV_$e@gUow{Rmvv8Ts){hQLSyOVyz^E_Tu1lE1{BUEuv>T38OMaV9$kCE zz~eAG%=SfbpmRd-f=`6T6~T1Lmb8b!vhE13>+EN4{BLS8e{^YD-znU(L&dSfPeYnZ z#LBz3c4(1xfLg+Y8)Xigt5~9omE&)lV&!=BmUkuaM^XuGs|~d-*@piqsoI1fr(9@{9kUmIH?O_tCM;v>g;qOmSbMIZ4<;!@4cl_^8!(Riez z4dP9Km`n`Y&klNO<=GhjjVO8#Lq`i-JMbj$izSrrVMH~jm3e|^;)5fM#ZUJUlqB@? z(&!hq|2c`SUF`g81iyrV9O}{g6NwHv_~kvdgnmgVAg%*)(&Z@OXOVH)|J|Z}3F#a| z3CB{Nocc$AorI6%m-pTh?hy@AAIZ*=U%m%w1CE-M{PKQWLizp*Bs`G}d%7A0dN(Bb zH?Ml=XWMtnZj^K20L1?~T8Le^h F|8FmD + +$0 is used to remove redundant sequences from self-blastn output. +blastn should be run with \" -evalue 1e-5 -outfmt \"6 qseqid sseqid +qlen slen length qstart qend sstart send pident evalue\" -max_target_seqs 1000\" + +"; + +die $usage if @ARGV!=4; +my ($fa,$IDEN,$blast_out,$prefix)=@ARGV; + +my %seq=readfa($fa); +my %seqL=readLength($fa); + +my @cluster; +my %fflag; +my %pflag; + +my $index=0; +my %now; +my $pre_q=""; + +open(IN,$blast_out) || die "Cannot open $blast_out!\n"; +while(){ + chomp; + my ($qname,$tname,$qlen,$tlen, $len,$qstart,$qend,$tstart,$tend,$iden,$evalue)=split /\t/,$_; + next if $qname eq $tname; + next if defined $fflag{$qname}; + $iden/=100; + if($qname eq $pre_q){ + if ($qlen>=$tlen){ + add_to_now($tname,$iden,$len,$tstart,$tend,$tlen); + } + else{ + add_to_now($tname,$iden,$len,$qstart,$qend,$qlen); + } + } + else{ + my $new_clus=init_item($qname); + $fflag{$qname}=1; + $pflag{$qname}=$index; + foreach my $k (keys(%now)){ + if($now{$k}->{iden}>$IDEN){ + if(defined $fflag{$k}){ + next if $fflag{$k}>=$now{$k}->{iden}; + $cluster[$pflag{$k}]->{$k}=0; + $new_clus->{$k}=1; + $fflag{$k}=$now{$k}->{iden}; + $pflag{$k}=$index; + } + else{ + $new_clus->{$k}=1; + $fflag{$k}=$now{$k}->{iden}; + $pflag{$k}=$index; + } + } + } + push @cluster, $new_clus; + $index++; + %now=(); + if ($qlen>=$tlen){ + add_to_now($tname,$iden,$len,$tstart,$tend,$tlen); + } + else{ + add_to_now($tname,$iden,$len,$qstart,$qend,$qlen); + } + } + $pre_q=$qname; +} +close IN; + +my $outcl=$prefix.".cluster"; +my $outfa=$prefix.".fa"; +my %rep; + +open(OUT,">$outcl"); +my $i=0; +for($i=0;$i<@cluster;$i++){ + my $l=0; + my $rep=""; + foreach my $k (keys(%{$cluster[$i]})){ + if($cluster[$i]->{$k}==1){ + if($seqL{$k}>$l){ + $rep=$k; + $l=$seqL{$k}; + } + } + } + $rep{$rep}=1; + print OUT "Group ",$i+1,": "; + foreach my $k (keys(%{$cluster[$i]})){ + print OUT " ",$k if $cluster[$i]->{$k}==1; + } + print OUT "\n"; +} +foreach my $k (keys(%seq)){ + if(!defined($fflag{$k})){ + $rep{$k}=1; + print OUT "Group $i: $k\n"; + $i++; + } +} +close OUT; + +open(OUT,">$outfa"); +open(IN,$fa); +my $f=0; +while(){ + chomp; + if(/^>(.+)$/){ + if(defined $rep{$1}){ + $f=1; + print OUT $_,"\n"; + } + } + else{ + print OUT $_,"\n" if $f==1; + } +} +close IN; +close OUT; + +################################################ +sub readfa{ + my %h; + open(IN,$_[0]); + while(){ + chomp; + $h{$1}=1 if(/^>(.+)$/); + } + close IN; + return %h; +} + +sub readLength{ + my %h; + open(IN,$_[0]); + my $name=""; + while(){ + chomp; + if(/^>(.+)$/){ + $name=$1; + $h{$name}=0; + } + else{ + $h{$name}+=length($_); + } + } + close IN; + return %h; +} + +sub init_item{ + my %h; + $h{$_[0]}=1; + return \%h; +} + +sub add_to_now{ + my ($tname,$iden,$len,$tstart,$tend,$tlen)=@_; + if(defined $now{$tname}){ + if(!check_overlap($now{$tname},$tstart,$tend)){ + push @{$now{$tname}->{start}},$tstart; + push @{$now{$tname}->{end}},$tend; + $now{$tname}->{iden}=$now{$tname}->{iden}+$iden*$len/$tlen; + } + } + else{ + $now{$tname}=init_h($iden*$len/$tlen,$tstart,$tend); + } +} + +sub init_h{ + my %h; + $h{iden}=$_[0]; + $h{start}=init_array($_[1]); + $h{end}=init_array($_[2]); + return \%h; +} + +sub init_array{ + my @a; + $a[0]=$_[0]; + return \@a; +} +sub check_overlap{ + my ($ad,$s,$e)=@_; + my $f=0; + for(my $i=0;$i<@{$ad->{start}};$i++){ + if(check_overlap_helper($s,$e,$ad->{start}->[$i],$ad->{end}->$i)){ + $f=1; + last; + } + } + close $f; +} + +sub check_overlap_helper{ + my ($a,$b,$c,$d)=@_; + if($a<$c){ + return 0 if $b<$c; + return 1 if $b>=$c; + } + elsif($a>$c){ + return 0 if $d<$a; + return 1 if $d>=$a; + } + else{ + return 1; + } +} diff --git a/bin/breakGCscaf.pl b/bin/breakGCscaf.pl new file mode 100755 index 0000000..08283cb --- /dev/null +++ b/bin/breakGCscaf.pl @@ -0,0 +1,69 @@ +#!/usr/bin/perl +#Created by Hu Zhiqiang, 2014-10-5 +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_m); +getopts("m:"); +my $usage="Usage: $0 [options] +This script is to break gap-closed scaffolds into contigs at consecutive N. + +Option: + -m the number of consecutive N to be broken down + default: 10 +"; +die $usage if @ARGV!=2; + +my $con_N=10; +$con_N=$opt_m if defined($opt_m); + +break_scaffolds(@ARGV,$con_N); + +sub break_scaffolds{ + my ($in,$out,$sepN)=@_; + my $sep=""; + for(my $i=1;$i<$sepN;$i++){ + $sep.="N"; + } + open(SCAF,$in)||die("Error09: cannot read file:$in\n"); + open(CONTIG,">$out")||die("Error10: cannot write file:$out\n"); + my $init=1; + my ($header,$seq); + while(my $line=){ + chomp $line; + if($line=~/^>/){ + if(!$init){ + split_and_print_seq($seq,$sep,$header); + ($header)=split /\s+/,$line; + $seq=""; + } + else{ + ($header)=split /\s+/,$line; + $seq=""; + $init=0; + } + } + else{ + $seq.=$line; + } + } + split_and_print_seq($seq,$sep,$header); + close SCAF; + close CONTIG; +} + +sub split_and_print_seq{ + my ($seq,$sep,$header)=@_; + my $i=0; + my @tmp=split /\Q$sep\EN+/,$seq; + foreach my $s (@tmp){ + next if length($s)==0; + $i++; + print CONTIG $header,"_",$i,"\n"; + for(my $j=0;$j0; + } +} + diff --git a/bin/ccov b/bin/ccov new file mode 100755 index 0000000000000000000000000000000000000000..fcd0362aeb3feedd8e5e8a0b3a36c0a0c5d14fc8 GIT binary patch literal 96120 zcmeFaeSB2K^#{Cx1fzl*EoiE!QCAI$HXzY#A(}`6cX5M}prTa+gg~f3VzNOLfnYYu zdR@hLsiC z3;F5zbMaE|n|mM=mwV4tNncOgNtexsgWUTou+P1_wewE8?ym8tsvP(3%Tj65W$-ai zrBm;vn-tu=n{=|iEX_g6J?E#2&b^y-l#NxO=qxMwzVQ%6S9h4YyL1#6>BbFJ_~R~0 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0h3g1&b94+pRmLlBH@KQhWbbL+bc2O|Hwhnn+K07Yt@rI@k3DWrVJBs$v;M&`|e8hu8o~&a$iB zi@XGNxNC+bq;{G}kqdqQVt}0sj8+t}U4dU}f4mCS`#SP5$5rHj4k9GJh2g z$aL7|$FF4mU4YUS4wYW*^H*U%_OsDNWh6PP^jMDOmlwa3rAn{f2T-AU&q-hl8tR_H zuj8NIAyVnpdjl#wB#{;W3QvVs;yJyOq~hxR0u>I*^u#~$srZ**)`uICsY1p2x8btGrP3=sx*ITK{^~uLu1b-f_U{`nm0pEYfo4n}+ec>;=`+bs(WL!7 zL`(5+lluY-Wcse8{B0_s3`=DGB}s6V{wqmv!Ij{d9#K3g3!cIu^KZmHI=W89e--{! qxmCHyJt*FB8@q045;?6Qqi48O{tATcifPk-+Ac6Fk`g3E+5Z3^d(b}s literal 0 HcmV?d00001 diff --git a/bin/filterNovelgene.pl b/bin/filterNovelgene.pl new file mode 100755 index 0000000..c03e110 --- /dev/null +++ b/bin/filterNovelgene.pl @@ -0,0 +1,349 @@ +#!/usr/bin/perl +#Created by Duan Zhongqu at 2018-11-5 +use strict; +use warnings; +use Getopt::Std; + +my $usage="Usage: $0 seq_file gff_file tra_file pro_file genome_ref tran_ref cdhit_exe blast_exe mkblastdb_exe repeat_exe gene_identity ref_identity thread_num out_dir\n"; + +die $usage if @ARGV!=14; + +my ($seq_file,$gff_file,$tra_file,$pro_file,$genome_ref,$tran_ref,$cdhit_exe,$blast_exe,$mkblastdb_exe,$repeat_exe,$gene_identity,$ref_identity,$thread_num,$out_dir)=@ARGV; + +my $log_file=$out_dir."FilterNovelGene.log"; +open(LOG,">$log_file")||die("Cannot write the file.\n"); +print LOG "\nCommand: $0 $seq_file $gff_file $tra_file $pro_file $genome_ref $tran_ref $cdhit_exe $blast_exe $mkblastdb_exe $repeat_exe $gene_identity $ref_identity $thread_num $out_dir\n\n"; +print LOG "\tInput file:\n\t$seq_file\n\t$gff_file\n\t$tra_file\n\t$pro_file\n\n"; +print LOG "\tReference information:\n\t$genome_ref\n\t$tran_ref\n\n"; +print LOG "\tOutput directory:\n\t$out_dir\n\n"; +print LOG "\tBinary executable file:\n\t$cdhit_exe\n\t$blast_exe\n\t$mkblastdb_exe\n\t$repeat_exe\n\n"; +print LOG "\tOptions:\n\tGene identity: $gene_identity\n\tReference identity: $ref_identity\n\tThread number: $thread_num\n\n"; + +#read the gff file and get the number of novel predicted genes. +my $raw_out_dir=$out_dir."raw/"; +mkdir($raw_out_dir); +my $filter_100bp_dir=$out_dir."100bps/"; +mkdir($filter_100bp_dir); +open(GFF,$gff_file)||die("Error9: cannot read the gff file.\n"); +my $new_gff_file=$raw_out_dir."maker.raw.gff"; +open(OUT1,">$new_gff_file")||die("Error10: cannot write the file: $new_gff_file.\n"); +my $raw_gene_map=$raw_out_dir."maker.gene.map"; +open(OUT,">$raw_gene_map")||die("Error10: cannot write the file: $raw_gene_map.\n"); +print OUT "sequence name\tstart\tend\tgene name\n"; +my $gene_map=$filter_100bp_dir."gene_100bps.map"; +open(OUT2,">$gene_map")||die("Error10: cannot write the file: $gene_map.\n"); +print OUT2 "sequence name\tstart\tend\tgene name\n"; +my $count_raw_gene=0; +my $count_gene=0; +print LOG "--------------------\nRead $gff_file file...\n\tall the annotation informations from maker will be selected and writtend into $new_gff_file.\n\tthe positions of each predicted gene were recorded in $raw_gene_map.\n"; +while(my $line=){ + chomp $line; + if($line=~/maker/){ + print OUT1 $line."\n"; + if($line=~/maker\tgene/){ + $count_raw_gene+=1; + my @string=split "\t",$line; + my $gene_length=$string[4]-$string[3]+1; + my @tmp=split ";",$string[8]; + my $gene_id=substr($tmp[0],3); + print OUT $string[0]."\t".$string[3]."\t".$string[4]."\t".$gene_id."\n"; + if($gene_length>=100){ + $count_gene+=1; + print OUT2 $string[0]."\t".$string[3]."\t".$string[4]."\t".$gene_id."\n"; + } + } + } +} +print LOG "\tthere are $count_raw_gene novel gene were predicted by the maker tools.\n"; +print LOG "\tof these, $count_gene genes are longer than 100 bp.\n\tthe positions of each predicted gene were recorded in $gene_map.\n"; +close GFF; +close OUT1; +close OUT2; +close OUT; + +#read the novel, transcript and protein sequences onto hash +my %novel_seq=readSeq($seq_file); +my %tran_seq=readSeq($tra_file); +my %prot_seq=readSeq($pro_file); +#obtain the gene sequences from novel sequences based on the gff file. +open(IN,$gene_map)||die("Error9: cannot read the file: $gene_map.\n"); +my $gene_file=$filter_100bp_dir."gene.100bps.fasta"; +open(OUT,">$gene_file")||die("Error10: cannot write the file: $gene_file.\n"); +readline IN; +my %gene_seq; +my %gene_length; +print LOG "\twrite these genes into $gene_file.\n"; +while(my $line=){ + chomp $line; + my @string=split "\t",$line; + my $name=$string[0]; + my $start=$string[1]; + my $end=$string[2]; + my $length=$end-$start+1; + my $gene_id=$string[3]; + my $all_seq=$novel_seq{$name}; + my $seq=substr($all_seq,$start-1,$length); + $gene_seq{$gene_id}=$seq; + $gene_length{$gene_id}=length($seq); + print OUT ">".$gene_id."\t".$name."\t".$start."\t".$end."\n".$seq."\n"; +} +close IN; +close OUT; +my $iden=$gene_identity*100; +print LOG "Done.\n--------------------\nRemoving the redundancy genes with sequence identity of ".$iden."%...\n"; +#remove the redundant gene sequence +my $rm_redundancy_dir=$out_dir."Non-redundancy/"; +mkdir ($rm_redundancy_dir); +my $cdhit_out=$rm_redundancy_dir."non.redundant.gene.fasta"; +my $cdhit_log=$rm_redundancy_dir."cdhit.log"; +my $com="$cdhit_exe -i $gene_file -o $cdhit_out -T $thread_num -c $gene_identity >$cdhit_log"; +system($com); +#Count the number of rest novel gene +my @non_redun_gene=extract_gene_name($cdhit_out); +my $non_redun_gene_count=@non_redun_gene; +print LOG "\tthere are $non_redun_gene_count novel genes after removing homology gene sequences in $cdhit_out.\n"; + +#align the novel sequence to reference genome seqeuces +print LOG "Done.\n-------------------\nAlign the gene sequences to reference genome...\n"; +my $genome_ref_dir=$out_dir."ref_genome/"; +mkdir($genome_ref_dir); +my $genome_db=$genome_ref_dir."blast_db_genome"; +my $genome_blast=$genome_ref_dir."non.redundant.gene.blast2genome"; +runblast($blast_exe,$mkblastdb_exe,$genome_ref,$genome_db,$cdhit_out,$genome_blast,$thread_num); + +#discard the gene could align to reference genome at the global identity cutoff 50% +my %gene_similar_genome=filterblast($genome_blast,\%gene_length); +my @gene_non_similar_genome=grep {!$gene_similar_genome{$_}} @non_redun_gene; +my $gene_non_similar_genome_count=@gene_non_similar_genome; +print LOG "\tthere are $gene_non_similar_genome_count novel genes after removing genes similar with the reference genome.\n"; +my $gene_non_similar_genome_file=$genome_ref_dir."Non-similar2genome.gene.fasta"; +my @genes=extractSub($cdhit_out,$gene_non_similar_genome_file,"gene",\@gene_non_similar_genome); +my $tran_non_similar_genome_file=$genome_ref_dir."Non-similar2genome.transcripts.fasta"; +my @tran_non_similar_genome=extractSub($tra_file,$tran_non_similar_genome_file,"transcripts",\@gene_non_similar_genome); +print LOG "Done.\n--------------------\nAlign the gene sequences to reference transcript...\n"; +#align the transcripts sequence to reference transcript sequences +my $tran_ref_dir=$out_dir."ref_tran/"; +mkdir($tran_ref_dir); +my $tran_db=$tran_ref_dir."blast_db_transcripts"; +my $tran_blast=$tran_ref_dir."non.similar2genome.transcripts.blast2transcript"; +runblast($blast_exe,$mkblastdb_exe,$tran_ref,$tran_db,$tran_non_similar_genome_file,$tran_blast,$thread_num); + +#discard the gene could align to transcript genome at the global identity cutoff 50% +my %tran_length; +while((my $key,my $value)=each %tran_seq){ + $tran_length{$key}=length($value); +} +my %tran_similar_genome=filterblast($tran_blast,\%tran_length); +my @tran_non_similar_transcript=grep {!$tran_similar_genome{$_}} @tran_non_similar_genome; +my %hash1; +foreach my $sub (@tran_non_similar_transcript){ + my $tmp=substr($sub,0,length($sub)-3); + if(grep /^$tmp$/,@gene_non_similar_genome){ + $hash1{$tmp}=1; + } +} +my @gene_non_similar_transcript=keys %hash1; +my $gene_non_similar_transcript_count=@gene_non_similar_transcript; +print LOG "\tthere are $gene_non_similar_transcript_count novel genes after removing genes similar with the reference transcript.\n"; +my $gene_non_similar_transcript_file=$tran_ref_dir."Non-similar2transcript.gene.fasta"; +@genes=extractSub($gene_non_similar_genome_file,$gene_non_similar_transcript_file,"gene",\@gene_non_similar_transcript); +my $tran_non_similar_transcript_file=$tran_ref_dir."Non-similar2transcript.transcripts.fasta"; +my @trans=extractSub($tran_non_similar_genome_file,$tran_non_similar_transcript_file,"transcript",\@gene_non_similar_transcript); +print LOG "Done.\n--------------------\nDetermine the full-length genes...\n"; +#define whether the novel gene is complete according to start codon and stop codon. +my %filtered_tran_seq=readSeq($tran_non_similar_transcript_file); +my %complete_gene_transcript_seq; +while((my $key,my $value)=each %filtered_tran_seq){ + my $start=substr($value,0,3); + my $end=substr($value,length($value)-3); + if(($start eq "ATG")&&($end eq "TAG"||$end eq "TAA"||$end eq "TGA")){ + $complete_gene_transcript_seq{$key}=$value; + } +} +my %hash2; +while((my $key,my $value)=each %complete_gene_transcript_seq){ + my $tmp=substr($key,0,length($key)-3); + $hash2{$tmp}=1; +} +my @complete_gene_name=keys %hash2; +my $complete_gene_dir=$out_dir."Full-length/"; +mkdir($complete_gene_dir); +my $complete_gene_file=$complete_gene_dir."Full-length.gene.fasta"; +@genes=extractSub($gene_non_similar_genome_file,$complete_gene_file,"gene",\@complete_gene_name); +my $complete_tran_file=$complete_gene_dir."Full-length.transcript.fasta"; +@trans=extractSub($tran_non_similar_transcript_file,$complete_tran_file,"transcript",\@complete_gene_name); +my $complete_gene_count=@complete_gene_name; +print LOG "\tthere are $complete_gene_count full-length novel genes.\n"; +print LOG "Done.\n--------------------\nRepeatmask the sequences of rest genes...\n"; +#repeat component of full-length novel gene. +my $repeat_out_dir=$out_dir."Repeat/"; +mkdir($repeat_out_dir); +$com="$repeat_exe -parallel $thread_num -species human -html -gff -dir $repeat_out_dir $complete_gene_file"; +system($com); +my $masked_gene_file=$repeat_out_dir."Full-length.gene.fasta.masked"; +my %masked_gene_seq=readSeq($masked_gene_file); +my %final_gene; +while((my $key,my $value)=each %masked_gene_seq){ + my $length=length($value); + my $count = $value =~ tr/N/N/; + if($count/$length<=0.5){ + $final_gene{$key}=1; + } +} +print LOG "Done.\n--------------------\nProcude final data set of novel genes...\n"; +my $final_gene_count=keys %final_gene; +print LOG "\tthere are $final_gene_count full-length novel genes.\n"; +my @final_gene_name=keys %final_gene; +my $final_out_dir=$out_dir."Final/"; +mkdir($final_out_dir); +my $final_gene_file=$final_out_dir."Final.gene.fasta"; +@genes=extractSub($complete_gene_file,$final_gene_file,"gene",\@final_gene_name); +my $final_tran_file=$final_out_dir."Final.transcript.fasta"; +@trans=extractSub($complete_tran_file,$final_tran_file,"transcript",\@final_gene_name); +my $final_prot_file=$final_out_dir."Final.protein.fasta"; +my @proteins=extractSub($pro_file,$final_prot_file,"protein",\@final_gene_name); +my $final_gff_file=$final_out_dir."Final.gff"; +open(IN,$new_gff_file)||die("Error09: cannot read the file: $new_gff_file"); +open(OUT,">$final_gff_file")||die("Errpr10: cannot write the file: $final_gff_file"); +while(my $line=){ + chomp $line; + my @string=split "\t", $line; + my @tmp=split ";", $string[8]; + my $name=substr($tmp[0],3,length($final_gene_name[0])); + if(grep /^$name$/, @final_gene_name){ + print OUT $line."\n"; + } +} +print LOG "Done.\n--------------------\n"; +print LOG "The final data set includes four files:\n\tgene sequences: $final_gene_file\t\ntranscript sequences: $final_tran_file\t\nprotein sequences: $final_prot_file\t\nannotation information: $final_gff_file.\n"; +close IN; +close OUT; +close LOG; + +sub readSeq{ + use strict; + use warnings; + my ($seq_file)=@_; + my %sequence; + open(IN,$seq_file)||die("Error09: Could not read file: $seq_file.\n"); + my $count=0; + my $seq; + my $name; + while(my $line=){ + chomp $line; + if($line=~/^>/){ + my @string=split /\s+/, $line; + if($count==0){ + $count+=1; + $name=substr($string[0],1); + } + else{ + $sequence{$name}=$seq; + $name=substr($string[0],1); + $seq=""; + } + } + else{ + $seq.=$line; + if(eof){ + $sequence{$name}=$seq; + } + } + } + close IN; + close OUT; + return %sequence; +} + +sub runblast{ + use strict; + use warnings; + my($blast_exe,$mkblastdb_exe,$ref,$db,$input,$output,$thread_num)=@_; + my $com="$mkblastdb_exe -in $ref -dbtype nucl -out $db"; + $com.="\n$blast_exe -query $input -db $db -out $output -outfmt 7 -max_target_seqs 1 -num_threads $thread_num\n"; + #print $com."\n"; + system("$com"); +} +1; + +sub extract_gene_name{ + use strict; + use warnings; + my ($input_file)=@_; + open(IN,$input_file)||die("Error09: cannot read the file: $input_file.\n"); + my @names; + while(my $line=){ + chomp $line; + if($line=~/^>/){ + my @string=split "\t",$line; + push @names, substr($string[0],1); + } + } + return @names; +} + +sub filterblast{ + use strict; + use warnings; + my ($blast_file,$gene_length)=@_; + my %gene_length=%$gene_length; + open(IN,$blast_file)||die("Error09: cannot read the file: $blast_file"); + my %names; + while(my $line=){ + chomp $line; + next if $line=~/^#/; + my @string=split "\t", $line; + my $name=$string[0]; + my $identity=$string[2]; + my $align_rate=$string[3]/$gene_length{$name}; + if($align_rate*$identity>=50){ + #if(($align_rate>=0.5)&&($identity>=80)){ + $names{$name}=1; + } + } + return %names; +} +1; +sub extractSub{ + use strict; + use warnings; + my ($input,$output,$type,$subsets)=@_; + my @subsets=@$subsets; + open(IN,$input)||die("Error09: cannot read the file: $input.\n"); + open(OUT,">$output")||die("Error10: cannot write the file: $output.\n"); + my $flag=0; + my %names; + while(my $line=){ + chomp $line; + if($line=~/^>/){ + my @string=split /\s+/,$line; + my $name; + my $tmp=substr($string[0],1); + $names{$tmp}=1; + if($type=~/gene/){ + $name=substr($string[0],1); + } + elsif($type=~/transcript/||$type=~/protein/){ + $name=substr($string[0],1,length($string[0])-4); + } + else{ + die("Please define the sequence type: 'gene', 'transcript' or 'protein'.\n"); + } + if(grep /^$name$/, @subsets){ + print OUT $line."\n"; + $flag=1; + } + else{ + $flag=0; + } + } + else{ + if($flag==1){ + print OUT $line,"\n"; + } + } + } + close IN; + close OUT; + return %names; +} diff --git a/bin/getTaxClass.pl b/bin/getTaxClass.pl new file mode 100755 index 0000000..10c108c --- /dev/null +++ b/bin/getTaxClass.pl @@ -0,0 +1,172 @@ +#!/usr/bin/perl +#Created by Duan Zhongqu at 2018-10-31. +#Revised by Duan Zhongqu at 2019-03-06. + +############################################################################################## +# This script firstly extracts all ACCESSION ID from blast result, # +# and then obtains the Taxonomy ID by the file: nucl_gb.accession2taxid, # +# finnaly, the lineage information were obtain according to rankedlineage.dmp # +############################################################################################## + +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_h); +getopts("h"); + +my $usage="\nUsage: $0 [options] + +$0 is used to obtain the taxonomic classification of each sequence from blast result. + +Necessary input description: + + The blast result of sequences aligning to nt database. + + The directory should contain two files: + 1. nucl_gb.accession2taxid, which is available in + ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/; + 2. rankedlineage.dmp, which is available in + https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/. + + The output directory. + +Options: + + -h Print this usage. + +"; + +die $usage if @ARGV!=3; +die $usage if $opt_h; +my ($blast_file,$info_dir,$out_dir)=@ARGV; + +die("Error01: Cannot find $blast_file\n") unless(-e $blast_file); +die("Error01: Cannot find $info_dir\n") unless(-e $info_dir); +unless($info_dir=~/\/$/){ + $info_dir.="/"; +} +unless($out_dir=~/\/$/){ + $info_dir.="/"; +} +my $accession2taxid=$info_dir."nucl_gb.accession2taxid"; +my $rankedlineage=$info_dir."rankedlineage.dmp"; + +unless(-e $accession2taxid){ + die("Error01: Cannot find the file: nucl_gb.accession2taxid in the $info_dir,\nplease download from the website: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/.") +} + +unless(-e $rankedlineage){ + die("Error01: Cannot find the file: rankedlineage.dmp in the $info_dir,\nplease download from the website: https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/.") +} + +#get the accession id of each alignment +open(IN,$blast_file)||die("Error9: cannot read the file: $blast_file!\n"); +my %accession; +while(my $line=){ +chomp $line; +next if $line=~/^#/; +my @string=split "\t",$line; +my @accession_version=split(/\./,$string[1]); + $accession{$accession_version[0]}=$string[1]; +} +close IN; +my $len1=keys %accession; +my $log_file=$out_dir."job.log"; +open(LOG,">$log_file")||die("Error10: cannot write the file $log_file.\n"); +print LOG "There are $len1 accession in the blast file.\n"; + +#get the related taxonomic id of accession id from accession2taxid file. +open(FILE1,$accession2taxid)||die("Error9: cannot read the file $accession2taxid!\n"); +my %acc_tax; +while(my $line=){ + chomp $line; + my @string=split "\t",$line; + if(exists $accession{$string[0]}){ + $acc_tax{$string[0]}=$string[2] + } +} +close FILE1; +my $len2=keys %acc_tax; +print LOG "\tOf these, $len2 accessiones could be found in the $accession2taxid.\n"; + +my $html_dir=$out_dir."html/"; +mkdir($html_dir); + +#obtain the taxonomix id of some accession id due to updating accession2taxid file. +if($len1!=$len2){ + my @acc_keys=keys %accession; + my @non=grep {!$acc_tax{$_}} @acc_keys; + my $len3=@non; + print LOG "\tIn total $len3 accessions have been removed in the file: $accession2taxid , and we will search them from NCBI.\n"; + foreach my $line (@non){ + my $html_file=$html_dir.$line.".html"; + system("wget https://www.ncbi.nlm.nih.gov/nuccore/$line -O $html_file"); + open(HTML,$html_file)||die("error with opening $html_file\n"); + while(){ + if($_ =~ /ORGANISM=(\d+)&/){ + my $tax_id=$1; + $acc_tax{$line}=$tax_id; + } + } + close HTML; + } +} + +#obtain taxonomic classification of each taxonomic id +my %taxid; +while((my $key, my $value)=each %acc_tax){ + $taxid{$value}=1; +} +my $len4=keys %taxid; +my $taxid_file=$out_dir."taxid.txt"; +print LOG "\nThere are $len4 taxid could be found.\n"; +open(TAX,">$taxid_file")||die("Error10: cannot write the file: $taxid_file.\n"); +while((my $key, my $value)=each %taxid){ + print TAX $key."\n"; +} +close TAX; + +my %source; +open(IN,$rankedlineage)||die("Cannot read the file: $rankedlineage.\n"); +while(my $line=){ + chomp $line; + my @string=split /\t\|\t/,$line; + if(exists($taxid{$string[0]})){ + $string[9]=~ s/\t|$//; + $source{$string[0]}.="superkingdom:".$string[9]."; "; + $source{$string[0]}.="kingdom:".$string[8]."; "; + $source{$string[0]}.="phylum:".$string[7]."; "; + $source{$string[0]}.="class:".$string[6]."; "; + $source{$string[0]}.="order:".$string[5]."; "; + $source{$string[0]}.="family:".$string[4]."; "; + $source{$string[0]}.="genus:".$string[3]."; "; + $source{$string[0]}.="species:".$string[2]."."; + } +} +close IN; + +my $len5=keys %source; +my $taxid_name_file=$out_dir."taxid.name"; +print LOG "There are $len5 taxid and name could be found.\n"; +open(NAME,">$taxid_name_file")||die("Error10: cannot write the file: $taxid_name_file.\n"); +while((my $key, my $value)=each %source){ + print NAME $key."\t".$value."\n"; +} + +my $out_file=$out_dir."accession.name"; +open(OUT,">$out_file")||die("Error10: cannot write the table: $out_file.\n"); +print OUT "accesion\taccession.version\ttaxid\tsource\n"; +while((my $key, my $value)=each %accession){ + #print $key."\n"; + my $taxonomy=$acc_tax{$key}; + my $records; + if(exists $source{$taxonomy}){ + $records=$source{$taxonomy}; + } + else{ + $records="Unclassified"; + } + print OUT $key."\t".$value."\t".$taxonomy."\t".$records."\n"; +} +close OUT; +close LOG; diff --git a/bin/getUnalnCtg.pl b/bin/getUnalnCtg.pl new file mode 100755 index 0000000..35cb7d8 --- /dev/null +++ b/bin/getUnalnCtg.pl @@ -0,0 +1,138 @@ +#!/usr/bin/perl +#Created by Hu Zhiqiang, 2014-9-5 +##Modefied by Duan Zhongqu, 2018-11-27 +##Extract both the fully unaligned contigs and partially unaligned contigs. +##Extract the coordinate of partially unaligned contigs locate in reference genome. + +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_h); +getopts("h"); + +my $usage="\nUsage: $0 [options] + +$0 is used to collect both fully unaligned contigs and partially unaligned contigs, and +collect the coords of the partially unaligned contigs. + +Necessary input description: + + contig_file Assembled contig fasta file. + + unaligned_info_file File including the info of unaligned contigs. + + coords_file File including the coords of contigs. + + output_prefix The prefix of outfiles. + + prefix A prefix added to the name of each contig. This is used + to mark which sample the contigs are from. + +Options: + -h Print this usage page. + +"; + +die $usage if @ARGV!=5; +die $usage if defined($opt_h); +my ($contig_file,$info_file,$coords_file,$output_prefix,$prefix)=@ARGV; + +#Check input file existence +die("Error01: Cannot find $contig_file\n") unless(-e $contig_file); +die("Error02: Cannot find $info_file\n") unless(-e $info_file); +die("Error02: Cannot find $coords_file\n") unless(-e $coords_file); + +#Define the output file +my $full_unalign_file=$output_prefix.".fully.contig"; +my $part_unalign_file=$output_prefix.".partially.contig"; +my $part_coords_file=$output_prefix.".partially.coords"; + +#Check existence of output file +print STDERR "Warning: $full_unalign_file file exists. Overwrite.\n" if -e $full_unalign_file; +print STDERR "Warning: $part_unalign_file file exists. Overwrite.\n" if -e $part_unalign_file; +print STDERR "Warning: $part_coords_file file exists. Overwrite.\n" if -e $part_coords_file; + +#read in unaligned info file and collect the fully unaligned contig names and the partially unaligned contig name. +my %full_unalign_names; +my %part_unalign_names; +open(IN,$info_file)||die("Error05: cannor read $info_file.\n"); +while(my $line=){ + chomp $line; + my @string=split "\t",$line; + if($string[3]=~/^full$/){ + $full_unalign_names{$string[0]}=0; + } + elsif($string[3]=~/^partial$/){ + $part_unalign_names{$string[0]}=0; + } +} + +#collect unaligned contigs from contig file +open(FULL,">$full_unalign_file") || die("Error04: Cannot write $full_unalign_file\n"); +open(PART,">$part_unalign_file") || die("Error04: Cannot write $part_unalign_file\n"); +if($contig_file=~/\.gz$/){ + open(CONTIG,"zcat $contig_file |") || die("Error05: Cannot read $contig_file\n"); +} +else{ + open(CONTIG,$contig_file) || die("Error05: Cannot read $contig_file\n"); +} +my $flag=0; +while(my $line=){ + if($line=~/^>(.+)$/){ + my $m=$1; + $m=~s/\s+/_/g; + if(defined($full_unalign_names{$m})){ + $flag=1; + $full_unalign_names{$m}=1; + print FULL ">$prefix:$m\n"; + } + elsif(defined($part_unalign_names{$m})){ + $flag=2; + $part_unalign_names{$m}=1; + print PART ">$prefix:$m\n"; + } + else{ + $flag=0; + } + } + else{ + print FULL $line if $flag==1; + print PART $line if $flag==2; + } +} +close CONTIG; +close FULL; +close PART; + +#Examine if all fully unaligned contigs are extracted +foreach my $key1 (keys(%full_unalign_names)){ + print STDERR "WARNING: Cannot find $key1 in $full_unalign_file\n" if $full_unalign_names{$key1}==0; +} + +#Examine if all partially unaligned contigs are extracted +foreach my $key2 (keys(%part_unalign_names)){ + print STDERR "WARNING: Cannot find $key2 in $part_unalign_file\n" if $part_unalign_names{$key2}==0; +} + +#Collect the coords of partially unaligned contigs from coords file. +open(IN,$coords_file)||die("Error05: Cannot read $coords_file"); +open(OUT,">$part_coords_file")||die("Error04: Cannot write $part_coords_file"); +print OUT "Query\tRef\tQuery.start\tQuery.end\tRef.start\tRef.end\tQuery.len\tRef.len\tIdentity"; +readline IN; +readline IN; +while(my $line=){ + chomp $line; + my @string=split /\s+/,$line; + if(exists($part_unalign_names{$string[12]})){ + $part_unalign_names{$string[12]}=0; + print OUT $prefix.":".$string[12]."\t".$string[11]."\t".$string[3]."\t".$string[4]."\t".$string[0]."\t".$string[1]."\t".$string[7]."\t".$string[6]."\t".$string[9]."\n"; + } +} +close IN; +close OUT; + +#Examine if all the partially unaligned contigs coords are extracted +foreach my $key3 (keys(%part_unalign_names)){ + print STDERR "WARNING: Cannot find $key3 in $part_unalign_file\n" if $part_unalign_names{$key3}==1; +} + diff --git a/bin/hupan b/bin/hupan new file mode 100755 index 0000000..cc1b4a0 --- /dev/null +++ b/bin/hupan @@ -0,0 +1,230 @@ +#!/usr/bin/perl +use strict; +use warnings; +use HUPANqualSta; +use HUPANtrim; +use HUPANmap; +use HUPANsamToBam; +use HUPANbamSta; +use HUPANassem; +use HUPANassemSta; +use HUPANunalnCtg; +use HUPANrmRdt; +use HUPANfastaSta; +use HUPANgeneCov; +use HUPANpTpG; +use HUPANgeneExist; +use HUPANbam2bed; +use HUPANsim; +use HUPANrmHigh; +use HUPANgetTaxClass; +use HUPANrmContaminate; +use HUPANblastAlign; +use HUPANsimSeq; +use HUPANsplitSeq; +use HUPANgenePre; +use HUPANmergeNovGene; +use HUPANfilterNovGene; + +checkPRE() if @ARGV==0; +PrintUsage() if @ARGV<1; + +my %commands=( + "qualSta" => 0, + "trim" => 0, + "alignRead" => 0, + "sam2bam" => 0, + "bamSta" => 0, + "assemble" => 0, + "assemSta" => 0, + "getUnalnCtg" => 0, + "rmRedundant" => 0, + "pTpG" => 0, + "geneCov" => 0, + "geneExist" => 0, + "subSample" => 0, + "gFamExist" => 0, + "bam2bed" => 0, + "fastaSta" => 0, + "sim" => 0, + "alignContig" => 0, + "extractSeq" => 0, + "getTaxClass" => 0, + "rmCtm" => 0, + "blastAlign" => 0, + "simSeq" => 0, + "splitSeq" => 0, + "genePre" => 0, + "mergeNovGene" => 0, + "filterNovGene" => 0 +); + +my $com=shift @ARGV; +if(defined $commands{$com}){ + $commands{$com}=1; +} +else{ + print STDERR "Invalid command: $com\n"; + PrintUsage(); +} + +if($commands{"qualSta"}){ + if(qualSta::checkQual(@ARGV)){ + qualSta::mergeFastqc(@ARGV); + } +} +elsif($commands{"trim"}){ + trim::trimFastq(@ARGV); +} +elsif($commands{"alignRead"}){ + align::map(@ARGV); +} +elsif($commands{"sam2bam"}){ + adjAlign::sam2bam(@ARGV); +} +elsif($commands{"bamSta"}){ + bamStat::bamsta(@ARGV); +} +elsif($commands{"assemble"}){ + assembly::assemble(@ARGV); +} +elsif($commands{"assemSta"}){ + assemStat::runQuast(@ARGV); +} +elsif($commands{"getUnalnCtg"}){ + unalnCtg::getUnaln(@ARGV); +} +elsif($commands{"rmRedundant"}){ + rmRDT::rmRDT(@ARGV); +} +elsif($commands{"fastaSta"}){ + fastaSta::sta(@ARGV); +} +elsif($commands{"geneCov"}){ + geneCov::cov(@ARGV); +} +elsif($commands{"pTpG"}){ + pTpG::pTpG(@ARGV); +} +elsif($commands{"geneExist"}){ + gExist::checkGeneExist(@ARGV); +} +elsif($commands{"subSample"}){ + gExist::subsetSample(@ARGV); +} +elsif($commands{"gFamExist"}){ + gExist::gE2gfE(@ARGV); +} +elsif($commands{"bam2bed"}){ + bam2cov::bam2bed(@ARGV); +} +elsif($commands{"sim"}){ + sim::simulation(@ARGV); + sim::pavPlot(@ARGV); +} +elsif($commands{"alignContig"}){ + rmHigh::alignContig(@ARGV); +} +elsif($commands{"extractSeq"}){ + rmHigh::extractSeq(@ARGV); +} +elsif($commands{"getTaxClass"}){ + getTaxClass::getTaxClass(@ARGV); +} +elsif($commands{"rmCtm"}){ + rmCTM::rmContaminate(@ARGV); +} +elsif($commands{"blastAlign"}){ + blastAlign::blastAlign(@ARGV); +} +elsif($commands{"simSeq"}){ + simSeq::simSeq(@ARGV); +} +elsif($commands{"splitSeq"}){ + splitSeq::splitSeq(@ARGV); +} +elsif($commands{"genePre"}){ + genePre::genePre(@ARGV); +} +elsif($commands{"mergeNovGene"}){ + mergeNovGene::mergeNovGene(@ARGV); +} +elsif($commands{"filterNovGene"}){ + filterNovGen::filterNovGen(@ARGV) +} + +sub PrintUsage{ + print STDERR "\nUsage: hupan ...\n\n"; + print STDERR "Available commands:\n"; + print STDERR "\tqualSta \tView the overall sequencing quality of a large number of files\n"; + print STDERR "\ttrim \tTrim or filter low-quality reads parallelly\n"; + print STDERR "\talignRead \tMap reads to a reference parallelly\n"; + print STDERR "\tsam2bam \tCovert alignments (.sam) to sorted .bam files\n"; + print STDERR "\tbamSta \tStatistics of parallel mapping\n"; + print STDERR "\tassemble \tAssemble reads parallelly\n"; + print STDERR "\talignContig \tAlign assembly results to a referenece parallelly\n"; + print STDERR "\textractSeq \tExtract contigs parallelly\n"; + print STDERR "\tassemSta \tStatistics of parallel assembly\n"; + print STDERR "\tgetUnalnCtg \tExtract the unaligned contigs from nucmer alignment (processed by quast)\n"; + print STDERR "\trmRedundant \tRemove redundant contigs of a fasta file\n"; + print STDERR "\tpTpG \tGet the longest transcripts to represent genes\n"; + print STDERR "\tgeneCov \tCalculate gene body coverage and CDS coverage\n"; + print STDERR "\tgeneExist \tDetermine gene presence-absence based on gene body coverage and CDS coverage\n"; + print STDERR "\tsubSample \tSelect subset of samples from gene PAV profile\n"; + print STDERR "\tgFamExist \tDetermine gene family presence-absence based on gene presence-absence\n"; + print STDERR "\tbam2bed \tCalculate genome region presence-absence from .bam\n"; + print STDERR "\tfastaSta \tCalculate statistics of fasta file\n"; + print STDERR "\tsim \tSimulation and plot of the pan-genome and the core genome\n"; + print STDERR "\tgetTaxClass \tObtain the taxonomic classification of sequences\n"; + print STDERR "\trmCtm \tDetect and discard the potentail contamination\n"; + print STDERR "\tblastAlign \tAlign sequences to target sequence by blast\n"; + print STDERR "\tsimSeq \tSimulate and plot the total size of novel sequences\n"; + print STDERR "\tsplitSeq \tSplit sequence file into multiple small size files\n"; + print STDERR "\tgenePre \tAb initio gene predict combining with RNA and protein evidence\n"; + print STDERR "\tmergeNovGene \tMerge maker result from multiple maker result files\n"; + print STDERR "\tfilterNovGene\tFilter the novel precited genes.\n"; + exit(-1); +} + +sub checkPRE{ + my $exec="ccov"; + my @path=split /:/,$ENV{PATH}; + my $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find ccov in your PATH!\n +") unless($fpflag); + + $exec="Rscript"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find Rscript in your PATH!\n +") unless($fpflag); + + + $exec="bam2cov"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find bam2cov in your PATH!\n +") unless($fpflag); +} + diff --git a/bin/hupanLSF b/bin/hupanLSF new file mode 100755 index 0000000..5e2d87a --- /dev/null +++ b/bin/hupanLSF @@ -0,0 +1,249 @@ +#!/usr/bin/perl +use strict; +use warnings; +use HUPANqualStaLSF; +use HUPANtrimLSF; +use HUPANmapLSF; +use HUPANsamToBamLSF; +use HUPANbamStaLSF; +use HUPANassemLSF; +use HUPANassemStaLSF; +use HUPANunalnCtgLSF; +use HUPANrmRdtLSF; +use HUPANfastaStaLSF; +use HUPANgeneCovLSF; +use HUPANpTpGLSF; +use HUPANgeneExistLSF; +use HUPANbam2bedLSF; +use HUPANsimLSF; +use HUPANrmHighLSF; +use HUPANgetTaxClassLSF; +use HUPANrmContaminateLSF; +use HUPANblastAlignLSF; +use HUPANsimSeqLSF; +use HUPANsplitSeqLSF; +use HUPANgenePreLSF; +use HUPANmergeNovGeneLSF; +use HUPANfilterNovGeneLSF; + +checkPRE() if @ARGV==0; +PrintUsage() if @ARGV<1; +my %commands=( + "qualSta" => 0, + "mergeQualSta" => 0, + "trim" => 0, + "alignRead" => 0, + "sam2bam" => 0, + "bamSta" => 0, + "assemble" => 0, + "assemSta" => 0, + "mergeAssemSta" => 0, + "getUnalnCtg" => 0, + "mergeUnalnCtg" => 0, + "rmRedundant" => 0, + "pTpG" => 0, + "geneCov" => 0, + "mergeGeneCov" => 0, + "geneExist" => 0, + "subSample" => 0, + "gFamExist" => 0, + "bam2bed" => 0, + "fastaSta" => 0, + "sim" => 0, + "alignContig" => 0, + "extractSeq" => 0, + "getTaxClass" => 0, + "rmCtm" => 0, + "blastAlign" => 0, + "simSeq" => 0, + "splitSeq" => 0, + "genePre" => 0, + "mergeNovGene" => 0, + "filterNovGene" => 0 +); + +my $com=shift @ARGV; +if(defined $commands{$com}){ + $commands{$com}=1; +} +else{ + print STDERR "Invalid command: $com\n"; + PrintUsage(); +} +if($commands{"qualSta"}){ + if(qualStaLSF::checkQual(@ARGV)){ + print STDERR "Run \"hupanLSF mergeQualSta\" command after all jobs are finished!\n"; + } +} +elsif($commands{"mergeQualSta"}){ + qualStaLSF::mergeFastqc(@ARGV); +} +elsif($commands{"trim"}){ + trim::trimFastq(@ARGV); +} +elsif($commands{"alignRead"}){ + align::map(@ARGV); +} +elsif($commands{"sam2bam"}){ + adjAlign::sam2bam(@ARGV); +} +elsif($commands{"bamSta"}){ + bamStat::bamsta(@ARGV); +} +elsif($commands{"assemble"}){ + assembly::assemble(@ARGV); +} +elsif($commands{"assemSta"}){ + assemStat::runQuast(@ARGV); +} +elsif($commands{"mergeAssemSta"}){ + assemStat::mergeAssemSta(@ARGV); +} +elsif($commands{"getUnalnCtg"}){ + unalnCtg::getUnaln(@ARGV); +} +elsif($commands{"mergeUnalnCtg"}){ + unalnCtg::mergeUnaln(@ARGV); +} +elsif($commands{"rmRedundant"}){ + rmRDT::rmRDT(@ARGV); +} +elsif($commands{"fastaSta"}){ + fastaSta::sta(@ARGV); +} +elsif($commands{"geneCov"}){ + geneCov::cov(@ARGV); +} +elsif($commands{"mergeGeneCov"}){ + geneCov::merge(@ARGV); +} +elsif($commands{"pTpG"}){ + pTpG::pTpG(@ARGV); +} +elsif($commands{"geneExist"}){ + gExist::checkGeneExist(@ARGV); +} +elsif($commands{"subSample"}){ + gExist::subsetSample(@ARGV); +} +elsif($commands{"gFamExist"}){ + gExist::gE2gfE(@ARGV); +} +elsif($commands{"bam2bed"}){ + bam2cov::bam2bed(@ARGV); +} +elsif($commands{"sim"}){ + sim::simulation(@ARGV); + sim::pavPlot(@ARGV); +} +elsif($commands{"alignContig"}){ + rmHigh::alignContig(@ARGV); +} +elsif($commands{"extractSeq"}){ + rmHigh::extractSeq(@ARGV); +} +elsif($commands{"getTaxClass"}){ + getTaxClass::getTaxClass(@ARGV); +} +elsif($commands{"rmCtm"}){ + rmCTM::rmContaminate(@ARGV); +} +elsif($commands{"blastAlign"}){ + blastAlign::blastAlign(@ARGV); +} +elsif($commands{"simSeq"}){ + simSeq::simSeq(@ARGV); +} +elsif($commands{"splitSeq"}){ + splitSeq::splitSeq(@ARGV); +} +elsif($commands{"genePre"}){ + genePre::genePre(@ARGV); +} +elsif($commands{"mergeNovGene"}){ + mergeNovGene::mergeNovGene(@ARGV); +} +elsif($commands{"filterNovGene"}){ + filterNovGen::filterNovGen(@ARGV) +} + +sub PrintUsage{ + print STDERR "\nUsage: hupanLSF ...\n\n"; + print STDERR "Available commands:\n"; + print STDERR "\tqualSta \tRun fastqc on a large number of files\n"; + print STDERR "\tmergeQualSta \tView the overall sequencing quality by combining fastqc outputs\n"; + print STDERR "\ttrim \tTrim or filter low-quality reads parallelly\n"; + print STDERR "\talignRead \tMap reads to a reference parallelly\n"; + print STDERR "\tsam2bam \tConvert alignments (.sam) to sorted .bam files\n"; + print STDERR "\tbamSta \tStatistics of parallel mapping\n"; + print STDERR "\tassemble \tAssemble reads parallelly\n"; + print STDERR "\talignContig \tAlign assembly results to a referenece parallelly\n"; + print STDERR "\textractSeq \tExtract contigs parallelly\n"; + print STDERR "\tassemSta \tStatistics of parallel assembly\n"; + print STDERR "\tmergeAssemSta\tMerge statistics of all indivduals to a single file\n"; + print STDERR "\tgetUnalnCtg \tExtract the unaligned contigs from nucmer alignment (processed by quast)\n"; + print STDERR "\tmergeUnalnCtg\tMerge the unaligned contigs into a single file\n"; + print STDERR "\trmRedundant \tRemove redundant contigs of a fasta file\n"; + print STDERR "\tpTpG \tGet the longest transcripts to represent genes\n"; + print STDERR "\tgeneCov \tCalculate gene body coverage and CDS coverage\n"; + print STDERR "\tmergeGeneCov \tMerge gene body coverage and cds coverage of each sample to two summary files\n"; + print STDERR "\tgeneExist \tDetermine gene presence-absence based on gene body coverage and CDS coverage\n"; + print STDERR "\tsubSample \tSelect subset of samples from gene PAV profile\n"; + print STDERR "\tgFamExist \tDetermine gene family presence-absence based on gene presence-absence\n"; + print STDERR "\tbam2bed \tCalculate genome region presence-absence from .bam\n"; + print STDERR "\tfastaSta \tCalculate statistics of fasta file\n"; + print STDERR "\tsim \tsimulation and plot of the pan-genome and the core genome\n"; + print STDERR "\tgetTaxClass \tObtain the taxonomic classification of sequence\n"; + print STDERR "\trmCtm \tDetect and discard the potentail contamination\n"; + print STDERR "\tblastAlign \tAlign sequences to target sequence by blast\n"; + print STDERR "\tsimSeq \tSimulate and plot the total size of novel sequences\n"; + print STDERR "\tsplitSeq \tSplit sequence file into multiple small size files\n"; + print STDERR "\tgenePre \tAb initio gene predict combining with RNA and protein evidence\n"; + print STDERR "\tmergeNovGene \tMerge maker result from multiple maker result files\n"; + print STDERR "\tfilterNovGene\tFilter the novel precited genes.\n"; + exit(-1); +} + + +sub checkPRE{ + my $exec="ccov"; + my @path=split /:/,$ENV{PATH}; + my $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find ccov in your PATH!\n +") unless($fpflag); + + $exec="Rscript"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find Rscript in your PATH!\n +") unless($fpflag); + + + $exec="bam2cov"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find bam2cov in your PATH!\n +") unless($fpflag); +} + diff --git a/bin/hupanSLURM b/bin/hupanSLURM new file mode 100755 index 0000000..2eb5215 --- /dev/null +++ b/bin/hupanSLURM @@ -0,0 +1,249 @@ +#!/usr/bin/perl +use strict; +use warnings; +use HUPANqualStaSLURM; +use HUPANtrimSLURM; +use HUPANmapSLURM; +use HUPANsamToBamSLURM; +use HUPANbamStaSLURM; +use HUPANassemSLURM; +use HUPANassemStaSLURM; +use HUPANunalnCtgSLURM; +use HUPANrmRdtSLURM; +use HUPANfastaStaSLURM; +use HUPANgeneCovSLURM; +use HUPANpTpGSLURM; +use HUPANgeneExistSLURM; +use HUPANbam2bedSLURM; +use HUPANsimSLURM; +use HUPANrmHighSLURM; +use HUPANgetTaxClassSLURM; +use HUPANrmContaminateSLURM; +use HUPANblastAlignSLURM; +use HUPANsimSeqSLURM; +use HUPANsplitSeqSLURM; +use HUPANgenePreSLURM; +use HUPANmergeNovGeneSLURM; +use HUPANfilterNovGeneSLURM; + +checkPRE() if @ARGV==0; +PrintUsage() if @ARGV<1; +my %commands=( + "qualSta" => 0, + "mergeQualSta" => 0, + "trim" => 0, + "alignRead" => 0, + "sam2bam" => 0, + "bamSta" => 0, + "assemble" => 0, + "assemSta" => 0, + "mergeAssemSta" => 0, + "getUnalnCtg" => 0, + "mergeUnalnCtg" => 0, + "rmRedundant" => 0, + "pTpG" => 0, + "geneCov" => 0, + "mergeGeneCov" => 0, + "geneExist" => 0, + "subSample" => 0, + "gFamExist" => 0, + "bam2bed" => 0, + "fastaSta" => 0, + "sim" => 0, + "alignContig" => 0, + "extractSeq" => 0, + "getTaxClass" => 0, + "rmCtm" => 0, + "blastAlign" => 0, + "simSeq" => 0, + "splitSeq" => 0, + "genePre" => 0, + "mergeNovGene" => 0, + "filterNovGene" => 0 +); + +my $com=shift @ARGV; +if(defined $commands{$com}){ + $commands{$com}=1; +} +else{ + print STDERR "Invalid command: $com\n"; + PrintUsage(); +} +if($commands{"qualSta"}){ + if(qualStaSLURM::checkQual(@ARGV)){ + print STDERR "Run \"hupanSLURM mergeQualSta\" command after all jobs are finished!\n"; + } +} +elsif($commands{"mergeQualSta"}){ + qualStaSLURM::mergeFastqc(@ARGV); +} +elsif($commands{"trim"}){ + trim::trimFastq(@ARGV); +} +elsif($commands{"alignRead"}){ + align::map(@ARGV); +} +elsif($commands{"sam2bam"}){ + adjAlign::sam2bam(@ARGV); +} +elsif($commands{"bamSta"}){ + bamStat::bamsta(@ARGV); +} +elsif($commands{"assemble"}){ + assembly::assemble(@ARGV); +} +elsif($commands{"assemSta"}){ + assemStat::runQuast(@ARGV); +} +elsif($commands{"mergeAssemSta"}){ + assemStat::mergeAssemSta(@ARGV); +} +elsif($commands{"getUnalnCtg"}){ + unalnCtg::getUnaln(@ARGV); +} +elsif($commands{"mergeUnalnCtg"}){ + unalnCtg::mergeUnaln(@ARGV); +} +elsif($commands{"rmRedundant"}){ + rmRDT::rmRDT(@ARGV); +} +elsif($commands{"fastaSta"}){ + fastaSta::sta(@ARGV); +} +elsif($commands{"geneCov"}){ + geneCov::cov(@ARGV); +} +elsif($commands{"mergeGeneCov"}){ + geneCov::merge(@ARGV); +} +elsif($commands{"pTpG"}){ + pTpG::pTpG(@ARGV); +} +elsif($commands{"geneExist"}){ + gExist::checkGeneExist(@ARGV); +} +elsif($commands{"subSample"}){ + gExist::subsetSample(@ARGV); +} +elsif($commands{"gFamExist"}){ + gExist::gE2gfE(@ARGV); +} +elsif($commands{"bam2bed"}){ + bam2cov::bam2bed(@ARGV); +} +elsif($commands{"sim"}){ + sim::simulation(@ARGV); + sim::pavPlot(@ARGV); +} +elsif($commands{"alignContig"}){ + rmHigh::alignContig(@ARGV); +} +elsif($commands{"extractSeq"}){ + rmHigh::extractSeq(@ARGV); +} +elsif($commands{"getTaxClass"}){ + getTaxClass::getTaxClass(@ARGV); +} +elsif($commands{"rmCtm"}){ + rmCTM::rmContaminate(@ARGV); +} +elsif($commands{"blastAlign"}){ + blastAlign::blastAlign(@ARGV); +} +elsif($commands{"simSeq"}){ + simSeq::simSeq(@ARGV); +} +elsif($commands{"splitSeq"}){ + splitSeq::splitSeq(@ARGV); +} +elsif($commands{"genePre"}){ + genePre::genePre(@ARGV); +} +elsif($commands{"mergeNovGene"}){ + mergeNovGene::mergeNovGene(@ARGV); +} +elsif($commands{"filterNovGene"}){ + filterNovGen::filterNovGen(@ARGV) +} + +sub PrintUsage{ + print STDERR "\nUsage: hupanSLURM ...\n\n"; + print STDERR "Available commands:\n"; + print STDERR "\tqualSta \tRun fastqc on a large number of files\n"; + print STDERR "\tmergeQualSta \tView the overall sequencing quality by combining fastqc outputs\n"; + print STDERR "\ttrim \tTrim or filter low-quality reads parallelly\n"; + print STDERR "\talignRead \tMap reads to a reference parallelly\n"; + print STDERR "\tsam2bam \tConvert alignments (.sam) to sorted .bam files\n"; + print STDERR "\tbamSta \tStatistics of parallel mapping\n"; + print STDERR "\tassemble \tAssemble reads parallelly\n"; + print STDERR "\talignContig \tAlign assembly results to a referenece parallelly\n"; + print STDERR "\textractSeq \tExtract contigs parallelly\n"; + print STDERR "\tassemSta \tStatistics of parallel assembly\n"; + print STDERR "\tmergeAssemSta\tMerge statistics of all indivduals to a single file\n"; + print STDERR "\tgetUnalnCtg \tExtract the unaligned contigs from nucmer alignment (processed by quast)\n"; + print STDERR "\tmergeUnalnCtg\tMerge the unaligned contigs into a single file\n"; + print STDERR "\trmRedundant \tRemove redundant contigs of a fasta file\n"; + print STDERR "\tpTpG \tGet the longest transcripts to represent genes\n"; + print STDERR "\tgeneCov \tCalculate gene body coverage and CDS coverage\n"; + print STDERR "\tmergeGeneCov \tMerge gene body coverage and cds coverage of each sample to two summary files\n"; + print STDERR "\tgeneExist \tDetermine gene presence-absence based on gene body coverage and CDS coverage\n"; + print STDERR "\tsubSample \tSelect subset of samples from gene PAV profile\n"; + print STDERR "\tgFamExist \tDetermine gene family presence-absence based on gene presence-absence\n"; + print STDERR "\tbam2bed \tCalculate genome region presence-absence from .bam\n"; + print STDERR "\tfastaSta \tCalculate statistics of fasta file\n"; + print STDERR "\tsim \tsimulation and plot of the pan-genome and the core genome\n"; + print STDERR "\tgetTaxClass \tObtain the taxonomic classification of sequences\n"; + print STDERR "\trmCtm \tDetect and discard the potentail contamination\n"; + print STDERR "\tblastAlign \tAlign sequences to target sequence by blast\n"; + print STDERR "\tsimSeq \tSimulate and plot the total size of novel sequences\n"; + print STDERR "\tsplitSeq \tSplit sequence file into multiple small size files\n"; + print STDERR "\tgenePre \tAb initio gene predict combining with RNA and protein evidence\n"; + print STDERR "\tmergeNovGene \tMerge maker result from multiple maker result files\n"; + print STDERR "\tfilterNovGene\tFilter the novel precited genes.\n"; + exit(-1); +} + + +sub checkPRE{ + my $exec="ccov"; + my @path=split /:/,$ENV{PATH}; + my $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find ccov in your PATH!\n +") unless($fpflag); + + $exec="Rscript"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find Rscript in your PATH!\n +") unless($fpflag); + + + $exec="bam2cov"; + @path=split /:/,$ENV{PATH}; + $fpflag=0; + foreach my $p (@path){ + $p.="/".$exec; + if(-e $p && -x $p){ + $fpflag=1; + last; + } + } + die("Can not find bam2cov in your PATH!\n +") unless($fpflag); +} + diff --git a/bin/linearK.pl b/bin/linearK.pl new file mode 100755 index 0000000..3317eff --- /dev/null +++ b/bin/linearK.pl @@ -0,0 +1,384 @@ +#!/usr/bin/perl +#Created by Hu Zhiqiang, 2014-10-5 +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_h $opt_t $opt_g $opt_s $opt_r $opt_w $opt_u $opt_c $opt_n $opt_k $opt_m); +getopts("ht:g:s:r:w:u:c:n:k:m:"); + +my $usage="Usage: $0 [options] + +$0 is to assembly paired FASTQ reads with SOAP DENOVO 2 with a dynamic K-mer. + +ATTENTION: Executable 1)SOAPdenovo-63mer, 2)SOAPdenovo-127mer and 3)GapCloser should EXIST in soap_denovo2_directory! + +Necessary input description: + + data_directory This directory should contain one or more pair of FASTQ files + with suffix of .fastq.gz or .fq.gz. The suffix can be changed with -s option. + + output_directory The output directory. + + soap_denovo2_directory Directory where soapdenovo2 program locates. SOAPdenovo-63mer, + SOAPdenovo-127mer and GapCloser should exist in this directory. + +Options: + -h Print this usage page. + + -t Threads used. + Default: 1 + + -g Genome size. Used to infer sequencing depth. + Default: 3000000000 (3Gb) + + -s Suffix of files within data_directory. + Default: .fastq.gz + + -r Parameters of linear function: Kmer=2*int(0.5*(a*Depth+b))+1. + The parameter should be input as \"a,b\". + Default: 0.76,20 + + -w Step-length of Kmer change. + Default: 2 + + -u Upper limmited times of Kmer change. This parameter is set to reduce + redundancy computation. + Default: 10 + + -c Parameters of soapdenovo2 config file. 8 parameters ligated by comma + 1)maximal read length + 2)average insert size + 3)if sequence needs to be reversed + 4)in which part(s) the reads are used + 5)use only first N bps of each read + 6)in which order the reads are used while scaffolding + 7)cutoff of pair number for a reliable connection (at least 3 for + short insert size) + 8)minimum aligned length to contigs for a reliable read location + (at least 32 for short insert size) + Default: 80,460,0,3,80,1,3,32 + + -n The minimum length of contigs. Contigs shorter than this length will + NOT be used when calculating N50. + Default: 100 + + -k Available Kmer range. Give comma-seperated lower bound and upper bound. + Default: 15,127 + + -m The number of consecutive Ns to be broken down to contigs.This is used + in the process break gapclosed scaffolds to contigs. + Default: 10. + +======================================================= +Any comments or bugs could be sent to Hu Zhiqiang: + doodlehzq\@sjtu.edu.cn. +======================================================= +"; + +die $usage if @ARGV!=3; +die $usage if defined($opt_h); +my ($data_dir,$out_dir,$tool_dir)=@ARGV; + +#check existence of output directory +# die("Error: output directory \"$out_dir\" already exists. +#To avoid overwriting of existing files. We kindly request that the +# output directory should not exist."); if -e $out_dir; + +#detect executables +$tool_dir.="/" unless $tool_dir=~/\/$/; +my $exec63=$tool_dir."SOAPdenovo-63mer"; +die("Cannot find $exec63 in directory $tool_dir\n") unless -e $exec63; +my $exec127=$tool_dir."SOAPdenovo-127mer"; +die("Cannot find $exec127 in directory $tool_dir\n") unless -e $exec127; +my $execgap=$tool_dir."GapCloser"; +die("Cannot find $execgap in directory $tool_dir\n") unless -e $execgap; + +#define thread number +my $thread_num=1; +$thread_num=$opt_t if defined($opt_t); + +#define file suffix +my $suffix=".fastq.gz"; +$suffix=$opt_s if defined($opt_s); + +#define genome size +my $gsize=3000000000; +$gsize=$opt_g if defined($opt_g); + +#define linear function of Kmer +my ($lin_a,$lin_b)=(0.76,20); +($lin_a,$lin_b)=split /,/,$opt_r if defined($opt_r); + +#define step of Kmer change +my $step=2; +$step=$opt_w if defined($opt_w); + +#define max iteration times +my $max_iter=10; +$max_iter=$opt_u if defined($opt_u); + +#define SOAPdenovo contig parameters +my ($max_rd_len,$avg_ins,$reverse_seq,$asm_flags,$rd_len_cutoff,$rank,$pair_num_cutoff,$map_len) + =(80,460,0,3,80,1,3,32); +($max_rd_len,$avg_ins,$reverse_seq,$asm_flags,$rd_len_cutoff,$rank,$pair_num_cutoff,$map_len) + =split /,/,$opt_c if defined($opt_c); + +#define the min length of contigs +my $min_contig_len=100; +$min_contig_len=$opt_n if defined($opt_n); + +#define Kmer range +my ($minKmer, $maxKmer)=(15,127); +($minKmer, $maxKmer)=split /,/,$opt_k if defined($opt_k); + +#define number of consecutive Ns +my $con_N=10; +$con_N=$opt_m if defined($opt_m); + +#adjust directory and create output directory +$data_dir.="/" unless($data_dir=~/\/$/); +$out_dir.="/" unless($out_dir=~/\/$/); +mkdir($out_dir); + +#read in files under data_directory +opendir(DATA,$data_dir) || die("Error01: can not read input data directory: $data_dir\n"); +my @files=readdir(DATA); +closedir DATA; + +#parse fastq pairs +my %fq_base; +foreach my $f (@files){ + next if $f=~/^\.+$/; + print STDERR "Warnig: $f without suffix: $suffix\n" unless $f=~/$suffix$/; + next unless $f=~/$suffix$/; + my $fb=substr($f,0,length($f)-length($suffix)-1); + $fq_base{$fb}=1 unless defined($fq_base{$fb}); +} + +#generate SOAPdenovo config +my $config_file=$out_dir."soap.config"; +open(CONFIG,">$config_file") || die("Error02: can not write soap config file:$config_file\n"); +print CONFIG "\#maximal read length\nmax_rd_len=$max_rd_len\n[LIB]\n\#average insert size\navg_ins=$avg_ins\n\#if sequence needs to be reversed\nreverse_seq=$reverse_seq\n\#in which part(s) the reads are used\nasm_flags=$asm_flags\n\#use only first 100 bps of each read\nrd_len_cutoff=$rd_len_cutoff\n\#in which order the reads are used while scaffolding\nrank=$rank\n\# cutoff of pair number for a reliable connection (at least 3 for short insert size)\npair_num_cutoff=$pair_num_cutoff\n\#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)\nmap_len=$map_len\n\#a pair of fastq file, read 1 file should always be followed by read 2 file\n"; +foreach my $b (keys(%fq_base)){ + my $forward=$data_dir.$b."1".$suffix; + my $reverse=$data_dir.$b."2".$suffix; + print STDERR "Warning: missed file: $forward\n" unless -e $forward; + print STDERR "Warning: missed file: $reverse\n" unless -e $reverse; + print STDERR "Warning: missed file: $reverse\n" unless(-e $forward && -e $reverse); + print CONFIG "q1=$forward\nq2=$reverse\n" if(-e $forward && -e $reverse); +} +close CONFIG; + +#calculate sequencing depth +my $base_number=0; +foreach my $b (keys(%fq_base)){ + my $forward=$data_dir.$b."1".$suffix; + my $reverse=$data_dir.$b."2".$suffix; + $base_number+=count_base_from_fq($forward); + $base_number+=count_base_from_fq($reverse); +} +my $depth=$base_number/$gsize; +print STDERR "Total base number: $base_number\n"; +print STDERR "Sequencing depth = $depth (Referense size=$gsize)\n"; + +#calculate init Kmer +my $Kmid=2*int(0.5*($lin_a*$depth+$lin_b))+1; +my $Klow=$Kmid-$step; +my $Khigh=$Kmid+$step; +print STDERR "Init Kmer = $Kmid\n"; + +#init assembly +my $Nmid=run_assembly($Kmid,$out_dir."K".$Kmid); +my $Nlow=run_assembly($Klow,$out_dir."K".$Klow); +my $Nhigh=run_assembly($Khigh,$out_dir."K".$Khigh); + +#interated assembly +my $iter_times=0; +while($Nmid<$Nlow || $Nmid<$Nhigh){ + $iter_times++; + if($Nmid<$Nhigh){ #Kmer goes higher + if($iter_times>$max_iter){ #check iteration times + print STDERR "Stop best Kmer selection: out of max iteration times($max_iter)\n"; + ($Kmid,$Khigh)=($Khigh,$Kmid); + ($Nmid,$Nhigh)=($Nhigh,$Nmid); + last; + } + if($Khigh+$step>$maxKmer){ #check Kmer region + print STDERR "Stop best Kmer selection: ouside the UP boundary of Kmer($maxKmer)\n"; + ($Kmid,$Khigh)=($Khigh,$Kmid); + ($Nmid,$Nhigh)=($Nhigh,$Nmid); + last; + } + $Klow=$Kmid; + $Nlow=$Nmid; + $Kmid=$Khigh; + $Nmid=$Nhigh; + $Khigh+=$step; + $Nhigh=run_assembly($Khigh,$out_dir."K".$Khigh); + } + elsif($Nmid<$Nlow){ #Kmer goes lower + if($iter_times>$max_iter){ #check iteration times + print STDERR "Stop best Kmer selection: out of max iteration times($max_iter)\n"; + ($Kmid,$Klow)=($Klow,$Kmid); + ($Nmid,$Nlow)=($Nlow,$Nmid); + last; + } + if($Klow-$step<$minKmer){ #check Kmer region + print STDERR "Stop best Kmer selection: ouside the DOWN boundary of Kmer($minKmer)\n"; + ($Kmid,$Klow)=($Klow,$Kmid); + ($Nmid,$Nlow)=($Nlow,$Nmid); + last; + } + $Klow=$Kmid; + $Nlow=$Nmid; + $Kmid=$Khigh; + $Nmid=$Nhigh; + $Khigh+=$step; + $Nhigh=run_assembly($Khigh,$out_dir."K".$Khigh); + } +} + +#adjust outputs +system("mv $out_dir"."K$Kmid/* $out_dir"); +print STDERR "Finished!\nIteration_time=$iter_times\nKmer(selected)=$Kmid\nN50(K=$Kmid)=$Nmid\n"; +exit; + + + +######################## sub routines ############################ + +sub count_base_from_fq{ #usage: count_base_from_fq(file_name) + my ($fq)=@_; + my $bn=0; + if($fq=~/\.gz$/){ + open(FQ,"zcat $fq |") ||die("Error07: cannot open gzipped file: $fq\n"); + } + else{ + open(FQ,"$fq") ||die("Error08: cannot open file: $fq\n"); + } + my $i=0; + while(){ + $i++; + chomp; + $bn+=length($_) if($i%4==2); + } + close FQ; + return $bn; +} + + +sub run_assembly{ #usage n50=run_assembly(k,outdir) + my ($kmer,$out)=@_; + print STDERR "Assembly with kmer=$kmer\n"; + mkdir($out) unless(-e $out); + +#run soap_denovo + my $com; + if($kmer<=63){ + $com=$exec63; + } + else{ + $com=$exec127; + } + $com.=" all -s $config_file -o $out/K$kmer -K $kmer -R -F -p $thread_num >$out/soap.log 2>&1"; + system($com); + +#run gapcloser + $com=$execgap; + $com.=" -b $config_file -a $out/K$kmer.scafSeq -o $out/K\Q$kmer\E.gcScafSeq -t $thread_num >$out/gapcloser.log 2>&1"; + system($com); + +#break gap closed scaffolds to contigs + break_scaffolds("$out/K\Q$kmer\E.gcScafSeq","$out/K\Q$kmer\E.gcContig",$con_N); + +#calculate N50 + + my $n50=calculate_N50("$out/K\Q$kmer\E.gcContig"); + print STDERR "N50(K=$kmer)=$n50\n"; + return $n50; +} + +sub break_scaffolds{ + my ($in,$out,$sepN)=@_; + my $sep=""; + for(my $i=1;$i<$sepN;$i++){ + $sep.="N"; + } + open(SCAF,$in)||die("Error09: cannot read file:$in\n"); + open(CONTIG,">$out")||die("Error10: cannot write file:$out\n"); + my $init=1; + my ($header,$seq); + while(my $line=){ + chomp $line; + if($line=~/^>/){ + if(!$init){ + split_and_print_seq($seq,$sep,$header); + ($header)=split /\s+/,$line; + $seq=""; + } + else{ + ($header)=split /\s+/,$line; + $seq=""; + $init=0; + } + } + else{ + $seq.=$line; + } + } + split_and_print_seq($seq,$sep,$header); + close SCAF; + close CONTIG; +} + +sub split_and_print_seq{ + my ($seq,$sep,$header)=@_; + my $i=0; + my @tmp=split /\Q$sep\EN+/,$seq; + foreach my $s (@tmp){ + next if length($s)==0; + $i++; + print CONTIG $header,"_",$i,"\n"; + for(my $j=0;$j0; + } +} + +sub calculate_N50{ #usage: n50=calculate_N50(contig_file) + open(CONTIG,$_[0])||die("Error11: cannot open file:$_[0]\n"); + my @len; + my $seq=""; + my $cl=0; + my $init=1; + while(){ + if(/^>/){ + if(!$init){ + push @len,$cl if($cl>=$min_contig_len); + $seq=""; + $cl=0; + } + else{ + $init=0; + } + } + else{ + chomp; + $cl+=length($_); + } + } + push @len,$cl if($cl>=$min_contig_len); + close CONTIG; + @len=sort{$a<=>$b}(@len); + my $total=0; + foreach my $v (@len){ + $total+=$v; + } + $total/=2; + my $cal=0; + for(my $i=0;$i<@len;$i++){ + $cal+=$len[$i]; + return $len[$i] if($cal>=$total); + } +} diff --git a/bin/pav_plot.R b/bin/pav_plot.R new file mode 100755 index 0000000..e54948c --- /dev/null +++ b/bin/pav_plot.R @@ -0,0 +1,94 @@ +#!/usr/bin/Rscript +argv <- commandArgs(TRUE) + + + +#PAV simulation result plotting +#By Yue Zhao and Zhiqiang Hu, 3/30/2016 + + +#packages +library(ggplot2) + + +#Function definition + +#summarySE +## Gives count, mean, standard deviation, standard error of the mean, and confidence interval (default 95%). +## data: a data frame. +## measurevar: the name of a column that contains the variable to be summariezed +## groupvars: a vector containing names of columns that contain grouping variables +## na.rm: a boolean that indicates whether to ignore NA's +## conf.interval: the percent range of the confidence interval (default is 95%) +summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE, + conf.interval=.95, .drop=TRUE) { + library(plyr) + + # New version of length which can handle NA's: if na.rm==T, don't count them + length2 <- function (x, na.rm=FALSE) { + if (na.rm) sum(!is.na(x)) + else length(x) + } + + # This does the summary. For each group's data frame, return a vector with + # N, mean, and sd + datac <- ddply(data, groupvars, .drop=.drop, + .fun = function(xx, col) { + c(N = length2(xx[[col]], na.rm=na.rm), + mean = mean (xx[[col]], na.rm=na.rm), + sd = sd (xx[[col]], na.rm=na.rm) + ) + }, + measurevar + ) + + # Rename the "mean" column + datac <- rename(datac, c("mean" = measurevar)) + + datac$se <- datac$sd / sqrt(datac$N) # Calculate standard error of the mean + + # Confidence interval multiplier for standard error + # Calculate t-statistic for confidence interval: + # e.g., if conf.interval is .95, use .975 (above/below), and use df=N-1 + ciMult <- qt(conf.interval/2 + .5, datac$N-1) + datac$ci <- datac$se * ciMult + + return(datac) +} + + + +#readSim: read simulation data +readSim <- function(file = NULL){ + DATA=read.table(file,sep="\t",header=T) + d1=summarySE(data = DATA,measurevar ="Pan",groupvars = "Time") + d1$Ave = d1$Pan + colnames(d1)[3] = "class" + d1$class = "pan" + + d2=summarySE(data = DATA,measurevar ="Core",groupvars = "Time") + d2$Ave = d2$Core + colnames(d2)[3] = "class" + d2$class = "core" + + d = rbind(d1,d2) + + return(d) +} + + + +#start processing data and plotting + +all=readSim(file=argv[1]) +plot1=paste(argv[1],"_PAV_plot.pdf",sep="") + +p<-ggplot(all, aes(x=Time, y=Ave, color = class)) +p=p+ +geom_errorbar(aes(ymin=Ave-se, ymax=Ave+se), width=.05, size=1, color = "black")+ +geom_line(size=1)+geom_point()+ +scale_y_continuous(name="Average number")+ +scale_x_continuous(name="line number") + +ggsave(plot1,p) + diff --git a/bin/plotNovelSeq.R b/bin/plotNovelSeq.R new file mode 100755 index 0000000..293d5a8 --- /dev/null +++ b/bin/plotNovelSeq.R @@ -0,0 +1,23 @@ +#!/usr/bin/Rscript +argv <- commandArgs(TRUE) + + + +#Novel sequence simulation result plotting +#Duan Zhongqu, 2018-10-21 + + +#packages +library(ggplot2) + +data<-read.table(argv[1],sep="\t",header = T) +data_dir<-argv[2] +library(ggplot2) +plot1<-paste(data_dir,"simNovelSeq.pdf",sep="") + +p<-ggplot(data = data,aes(x=Sample.number,y=Sequence.length/1000000)) +p=p+ + geom_point(col="red",size=1.5)+xlab("Number of individuals")+ylab("Total length (Mb)")+theme_bw()+ + theme(axis.text=element_text(size=20,face="bold",colour = "black"),axis.title=element_text(size=20,face="bold",colour = "black"))+ + xlim(0,max(data$Sample.number))+ylim(0,max(data$Sequence.length)/1000000) +ggsave(plot1,p) diff --git a/bin/plotQual.R b/bin/plotQual.R new file mode 100755 index 0000000..f1a986b --- /dev/null +++ b/bin/plotQual.R @@ -0,0 +1,14 @@ +#!/usr/bin/Rscript +argv <- commandArgs(TRUE) +library("ggplot2") +library("reshape2") +d=read.table(argv[1],header=T) +d1=melt(d) +plot1=paste(argv[1],"_heatmap.pdf",sep="") +d1$variable=factor(d1$variable,levels=rev(levels(d1$variable))) +k=ggplot(data=d1)+geom_tile(aes(x=Sample,y=variable,fill=value))+ + scale_x_discrete(name="")+scale_y_discrete(name="")+ + scale_fill_gradient2(name="",low="red",mid="gold",high="darkgreen", + breaks=c(-1,0,1),labels=c("FAIL","WARNING","PASS"))+theme(axis.text.x=element_text(angle=90)) +ggsave(plot1,k) + diff --git a/bin/rmCtm.pl b/bin/rmCtm.pl new file mode 100755 index 0000000..a2fad42 --- /dev/null +++ b/bin/rmCtm.pl @@ -0,0 +1,221 @@ +#!/usr/bin/perl +#Created by Duan Zhongqu, 2018-10-22 +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_h); +getopts("h"); +my $usage="\nUsage: $0 [options] + +$0 is used to detect and discard the potentail contaminated sequence. + +Necessary input description: + + sequence_file The sequence file. + + blast_file The blast result of sequence file. + + accession_file The accession file. + + output_directory Both final output files and intermediate results + will be found in this directory. To avoid + overwriting of existing files. We kindly request + that the output_directory should not exist. It is + to say, this directory will be created by the + script itself. + + min_length The minimum alignment. + + min_identity The minimun identity. + +Options: + + -h Print this usage page. + +"; + +die $usage if @ARGV!=6; +die $usage if defined($opt_h); +my ($seq_file,$blast_file,$accession_file,$out_dir,$min_length,$min_identity)=@ARGV; + +#adjust directory names and create output directory +$out_dir.="/" unless($out_dir=~/\/$/); +mkdir($out_dir); +my $log_file=$out_dir."RemoveContaminate.log"; + +#Classify the accessions of target sequences according to the orangism information +open(IN,$accession_file)||die("Error9: cannot read the file: $accession_file!\n"); +my %accession_Human; +my %accession_OtherPrimate; +my %accession_Microbiology; +my %accession_Other; +my $count_Human=0; +my $count_OtherPrimate=0; +my $count_Microbiology=0; +my $count_Other=0; +while(my $line=){ + chomp $line; + my @string=split "\t", $line; + if($string[3]=~/genus:Homo/){ + $accession_Human{$string[1]}=$string[2]; + $count_Human+=1; + } + elsif($string[3]=~/order:Primates/){ + $accession_OtherPrimate{$string[1]}=$string[2]; + $count_OtherPrimate+=1; + } + elsif($string[3]=~/superkingdom:Viruses/||$string[3]=~/superkingdom:Bacteria/||$string[3]=~/superkingdom:Archaea/){ + $accession_Microbiology{$string[1]}=$string[2]; + $count_Microbiology+=1; + } + else{ + $accession_Other{$string[1]}=$string[2]; + $count_Other+=1; + } +} +close IN; +my $count_total=$count_Human+$count_OtherPrimate+$count_Microbiology+$count_Other; +open(LOG,">$log_file")||die("Error10: cannot write the file: $log_file.\n"); +print LOG "Accession information:\n"; +print LOG "In total, $count_total accessiones in the '$accession_file' file, of these\n\t$count_Human are belong to human;\n\t$count_OtherPrimate are belong to other primates;\n\t$count_Microbiology are belong to microbiology (including bacteria, virses and archaes);\n\tand $count_Other are belong to other orangism (including non-primate animals and plants).\n\n"; +close LOG; +#Classify the contigs according to the blast result +my %contig_Human; +my %contig_OtherPrimate; +my %contig_Microbiology; +my %contig_Other; +open(IN,$blast_file)||die("Error9: cannot read the file: $blast_file!\n"); +while(my $line=){ + chomp $line; + next if $line=~/^#/; + my @string=split "\t",$line; + if((int($string[2])>=$min_identity)&&($string[3]>=$min_length)){ + if(exists($accession_Human{$string[1]})){ + $contig_Human{$string[0]}=$string[1]; + } + elsif(exists($accession_OtherPrimate{$string[1]})){ + $contig_OtherPrimate{$string[0]}=$string[1]; + } + elsif(exists($accession_Microbiology{$string[1]})){ + $contig_Microbiology{$string[0]}=$string[1]; + } + elsif(exists($accession_Other{$string[1]})){ + $contig_Other{$string[0]}=$string[1]; + } + else{ + print STDERR ("Warning: $string[1] have not in $accession_file\n"); + } + } +} +close IN; + +#Output the classified contigs +open(IN,$seq_file)||die("Error9: cannot read the file: $seq_file!\n"); +my $seq_orangism_file=$out_dir."sequence.orangism.txt"; +my $Human_seq_file=$out_dir."human.fa"; +my $OtherPrimate_seq_file=$out_dir."other_primate.fa"; +my $Microbiology_seq_file=$out_dir."microbiology.fa"; +my $Other_seq_file=$out_dir."other.fa"; +my $NotInNt_seq_file=$out_dir."not_in_nt.fa"; +my $Novel_seq_file=$out_dir."novel_sequence.fa"; +open(OUT,">$seq_orangism_file")||die("Error10: cannot write the file: $seq_orangism_file.\n"); +open(OUT1,">$Human_seq_file")||die("Error10: cannot write the file: $Human_seq_file.\n"); +open(OUT2,">$OtherPrimate_seq_file")||die("Error10: cannot write the file: $OtherPrimate_seq_file.\n"); +open(OUT3,">$Microbiology_seq_file")||die("Error10: cannot write the file: $Microbiology_seq_file.\n"); +open(OUT4,">$Other_seq_file")||die("Error10: cannot write the file: $Other_seq_file.\n"); +open(OUT5,">$NotInNt_seq_file")||die("Error10: cannot write the file: $NotInNt_seq_file.\n"); +open(NOVEL,">$Novel_seq_file")||die("Error10: cannot write the file: $Novel_seq_file.\n"); +my $flag=0; +my $count_contig_Human=0; +my $count_contig_OtherPrimate=0; +my $count_contig_Microbiology=0; +my $count_contig_Other=0; +my $count_contig_NotInNt=0; +my $length_contig_Human=0; +my $length_contig_OtherPrimate=0; +my $length_contig_Microbiology=0; +my $length_contig_Other=0; +my $length_contig_NotInNt=0; +while(my $line=){ + chomp $line; + if($line=~/^>/){ + my @string=split /\s+/,$line; + my $name=substr($string[0],1,length($string[0])-1); + if(exists($contig_Human{$name})){ + print OUT $name."\t".$contig_Human{$name}."\t"."human\n"; + print OUT1 $line."\n"; + print NOVEL $line."\n"; + $count_contig_Human+=1; + $flag=1; + } + elsif(exists($contig_OtherPrimate{$name})){ + print OUT $name."\t".$contig_OtherPrimate{$name}."\t"."other primate\n"; + print OUT2 $line."\n"; + print NOVEL $line."\n"; + $count_contig_OtherPrimate+=1; + $flag=2; + } + elsif(exists($contig_Microbiology{$name})){ + print OUT $name."\t".$contig_Microbiology{$name}."\t"."microbiology\n"; + print OUT3 $line."\n"; + $count_contig_Microbiology+=1; + $flag=3; + } + elsif(exists($contig_Other{$name})){ + print OUT $name."\t".$contig_Other{$name}."\t"."other\n"; + print OUT4 $line."\n"; + $count_contig_Other+=1; + $flag=4; + } + else{ + print OUT $name."\t--\t"."not in nt database\n"; + print OUT5 $line."\n"; + print NOVEL $line."\n"; + $count_contig_NotInNt+=1; + $flag=5; + } + } + else{ + if($flag==1){ + print OUT1 $line."\n"; + print NOVEL $line."\n"; + $length_contig_Human+=length($line); + } + elsif($flag==2){ + print OUT2 $line."\n"; + print NOVEL $line."\n"; + $length_contig_OtherPrimate+=length($line); + } + elsif($flag==3){ + print OUT3 $line."\n"; + $length_contig_Microbiology+=length($line); + } + elsif($flag==4){ + print OUT4 $line."\n"; + $length_contig_Other+=length($line); + } + elsif($flag==5){ + print OUT5 $line."\n"; + print NOVEL $line."\n"; + $length_contig_NotInNt+=length($line); + } + } +} +close OUT1; +close OUT2; +close OUT3; +close OUT4; +close OUT5; +close NOVEL; +my $count_contig_total=$count_contig_Human+$count_contig_OtherPrimate+$count_contig_Microbiology+$count_contig_Other+$count_contig_NotInNt; +my $length_contig_total=$length_contig_Human+$length_contig_OtherPrimate+$length_contig_Microbiology+$length_contig_Other+$length_contig_NotInNt; +open(LOG,">>$log_file")||die("Error10: cannot write the file: $log_file.\n"); +print LOG "Result summary:\n"; +print LOG "Type\tNumber\tLength\n"; +print LOG "Human\t$count_contig_Human\t$length_contig_Human\n"; +print LOG "Other Primate\t$count_contig_OtherPrimate\t$length_contig_OtherPrimate\n"; +print LOG "Microbiology\t$count_contig_Microbiology\t$length_contig_Microbiology\n"; +print LOG "Other\t$count_contig_Other\t$length_contig_Other\n"; +print LOG "Not in nt database\t$count_contig_NotInNt\t$length_contig_NotInNt\n"; +print LOG "Total\t$count_contig_total\t$length_contig_total\n"; +close LOG; diff --git a/lib/HUPANgeneCovSLURM.pm b/lib/HUPANgeneCovSLURM.pm index 0521712..0f2d973 100644 --- a/lib/HUPANgeneCovSLURM.pm +++ b/lib/HUPANgeneCovSLURM.pm @@ -120,7 +120,7 @@ foreach my $s (@sample){ open(JOB,">$job_file")||die("Error05: Unable to create job file: $job_file\n"); print JOB "\#!/bin/bash\n"; print JOB "\#SBATCH --job-name=$s","_genesta\n"; #job name - print JOB "\#SBATCH -p $opt_q\n" if defined $opt_q; #queue name in the submission system + # print JOB "\#SBATCH -p $opt_q\n" if defined $opt_q; #queue name in the submission system print JOB "\#SBATCH --output=$out_file\n"; #stdout print JOB "\#SBATCH --error=$err_file\n"; #stderr print JOB "\#SBATCH -n $thread_num\n"; #thread number diff --git a/lib/HUPANmapSLURM.pm b/lib/HUPANmapSLURM.pm index a27d610..b5a36c9 100644 --- a/lib/HUPANmapSLURM.pm +++ b/lib/HUPANmapSLURM.pm @@ -207,7 +207,7 @@ foreach my $s (@sample){ # print JOB "\#SBATCH -p fat\n"; #stderr print JOB "\#SBATCH -n $thread_num\n"; #thread number print JOB "\#SBATCH --ntasks-per-node=$thread_num\n"; - print JOB "\#SBATCH --time=24:00:00\n"; + print JOB "\#SBATCH --time=36:00:00\n"; print JOB "$com\n"; #commands close JOB; system("sbatch $job_file"); #submit job diff --git a/lib/HUPANpTpGSLURM.pm b/lib/HUPANpTpGSLURM.pm index 1ca1eb3..13de76c 100644 --- a/lib/HUPANpTpGSLURM.pm +++ b/lib/HUPANpTpGSLURM.pm @@ -1,4 +1,7 @@ #!/usr/bin/perl + +# This is the script for MAKER produced annotations! + package pTpG; sub pTpG{ @@ -50,12 +53,16 @@ while(my $line=){ if($format eq "gff"){ my @string=split /[;|=]/,$record; if($type eq "gene"){ - if($string[5] eq "protein_coding"){ - $pre_gid=$string[3]; + $pre_gid=$string[1]; + $pre_tid=$string[1]; + print OUT "$chr\t$source\t$type\t$start\t$end\t$score\t$sym\t$phase\tgene_id \"$pre_gid\"; transcript_id \"$pre_tid\";\n"; + }elsif($type eq "mRNA"){ + if($string[3] eq $pre_gid){ + $pre_gid=$string[1]; } }else{ - if($string[5] eq $pre_gid){ - $pre_tid=$string[7]; + if($string[3] eq $pre_gid){ + $pre_tid=$string[3]; print OUT "$chr\t$source\t$type\t$start\t$end\t$score\t$sym\t$phase\tgene_id \"$pre_gid\"; transcript_id \"$pre_tid\";\n"; } } diff --git a/lib/HUPANrmHighSLURM.pm b/lib/HUPANrmHighSLURM.pm index 612332f..4075e00 100644 --- a/lib/HUPANrmHighSLURM.pm +++ b/lib/HUPANrmHighSLURM.pm @@ -152,6 +152,7 @@ foreach my $s (@sample){ print JOB "\#SBATCH -n $thread_num\n"; #thread number print JOB "\#SBATCH --ntasks-per-node=$thread_num\n\n"; #use the same node print JOB "\#SBATCH --time=96:00:00\n"; # set time + print JOB "\#SBATCH --mem=110GB\n"; print JOB "$com\n"; #commands close JOB; system("sbatch $job_file"); #submit job diff --git a/lib/HUPANsimSeqSLURM.pm b/lib/HUPANsimSeqSLURM.pm index 74d83d2..f1a8d32 100644 --- a/lib/HUPANsimSeqSLURM.pm +++ b/lib/HUPANsimSeqSLURM.pm @@ -131,7 +131,7 @@ Options: my $j=int(rand(scalar(@samples))); my $sample=$samples[$j]; splice @samples,$j,1; - my $individual_file=$data_dir.$sample."/".$sample.".fa"; + my $individual_file=$data_dir.$sample."/".$sample.".fully.contig"; my $num=$i+1; my $contig_file=$simulation_dir.$num."_raw.fa"; my $com="cp $individual_file $contig_file"; @@ -142,11 +142,11 @@ Options: my $com="\ncp $individual_file $in_file"; my $outfile=$simulation_dir."1_non.redundant.fa"; $com.="\n$exe -i $in_file -o $outfile -T $thread_num -c $iden"; - $com.="\nfor((\$i=2;\$i<=".@sample.";\$i++));\ndo\nk=\$((\$i-1));"; - $individual_file=$simulation_dir."\$i_raw.fa"; - my $novel_file=$simulation_dir."\$k_non.redundant.fa"; + $com.="\nfor((i=2;i<=".@sample.";i++));\ndo\nk=\$((\$i-1));"; + $individual_file=$simulation_dir."\${i}_raw.fa"; + my $novel_file=$simulation_dir."\${k}_non.redundant.fa"; $com.="\ncat $individual_file $novel_file >$in_file"; - $outfile=$simulation_dir."\$i_non.redundant.fa"; + $outfile=$simulation_dir."\${i}_non.redundant.fa"; $com.="\n$exe -i $in_file -o $outfile -T $thread_num -c $iden"; $com.="\ndone;"; #print $com."\n"; @@ -164,6 +164,8 @@ Options: print JOB "\#SBATCH --error=$err_file\n"; #stderr print JOB "\#SBATCH -n $thread_num\n"; #thread number print JOB "\#SBATCH --ntasks-per-node=$thread_num\n"; + print JOB "\#SBATCH --time=330:00:00\n"; + print JOB "\#SBATCH --mem=10GB\n"; print JOB "$com\n"; #commands close JOB; system("sbatch $job_file"); #submit job diff --git a/lib/originalHUPANpTpGSLURM.pm b/lib/originalHUPANpTpGSLURM.pm new file mode 100644 index 0000000..1ca1eb3 --- /dev/null +++ b/lib/originalHUPANpTpGSLURM.pm @@ -0,0 +1,232 @@ +#!/usr/bin/perl +package pTpG; + +sub pTpG{ +use strict; +use warnings; +use Getopt::Std; +use vars qw($opt_h $opt_e $opt_f); +getopts("hef"); +my $usage="\nUsage: hupan pTpG [options] inputfile outputfile + +hupan pTpG is used to obtain the longest transcript of each protein-coding genes from annotation file. +Notice: a file named \"protein_coding.gtf\" will be automatically prodcued to store all the protein-coding genes. + +Necessary input description: + + inputfile Annotation file. Default: \"gff\" format. + If the annotation file is \"gtf\", please use the option \"-f\". + + outputfile Outputfile. + +Options: + + -h Print this usage page. + + -e Check \"exon\" length instead of check \"CDS\" length. + + -f The annotation file is \"gtf\" format. +"; + +#print @ARGV; +die $usage if @ARGV!=2; +die $usage if defined($opt_h); +my ($gff_file,$out_file)=@ARGV; + +my $format="gff"; +$format="gtf" if defined($opt_f); + +open(IN,$gff_file)||die("Error: cannot read the file: $gff_file.\n"); +my $temp_file="protein_coding.gtf"; +open(OUT,">$temp_file")||die("Error: cannot write the file: $temp_file.\n"); +my $pre_gid=""; +my $pre_tid=""; +my %genes; + +while(my $line=){ + chomp $line; + next if $line=~/^#/; + my ($chr,$source,$type,$start,$end,$score,$sym,$phase,$record)=split /\t/,$line; + if($format eq "gff"){ + my @string=split /[;|=]/,$record; + if($type eq "gene"){ + if($string[5] eq "protein_coding"){ + $pre_gid=$string[3]; + } + }else{ + if($string[5] eq $pre_gid){ + $pre_tid=$string[7]; + print OUT "$chr\t$source\t$type\t$start\t$end\t$score\t$sym\t$phase\tgene_id \"$pre_gid\"; transcript_id \"$pre_tid\";\n"; + } + } + }else{ + if($type eq "gene"){ + $record=~/(gene_id \"[^\"]+\"); (gene_type \"[^\"]+\")/; + if($2 eq "gene_type \"protein_coding\""){ + $pre_gid=$1; + } + }else{ + $record=~/(gene_id \"[^\"]+\"); (transcript_id \"[^\"]+\")/; + if($1 eq $pre_gid ){ + $pre_tid=$2; + print OUT "$chr\t$source\t$type\t$start\t$end\t$score\t$sym\t$phase\t$pre_gid; $pre_tid;\n"; + } + } + } +} +close IN; +close OUT; + +my ($Vec, $num) = @{Read_GTF($temp_file)}; + +#open(OUT,">$out"); +open(OUT,">$out_file")||die("Error: cannot write the file: $out_file.\n"); +foreach my $d (@{$Vec}){ + my $target=$d->[0]; + my $len=getLen($d->[0]); + for(my $i=1;$i<@{$d};$i++){ + my $nlen=getLen($d->[$i]); + if($nlen>$len){ + $len=$nlen; + $target=$d->[$i]; + } + } + if($len!=0){ + OutputTran($target); + } +} + +exit; + + +########## sub routines ########### +sub getLen{ + my ($d)=@_; + my $len=0; + foreach my $k (@{$d}){ + if(defined $opt_e){ + if($k->{type} eq "exon"){ + $len+=$k->{end}-$k->{start}+1; + } + } + else{ + if($k->{type} eq "CDS" ||$k->{type} eq "stop_codon"){ + $len+=$k->{end}-$k->{start}+1; + } + } + } + return $len; +} + +sub OutputTran{ #\@tvec,$name ,output file + my ($ad) = @_; + my $d1; + for($d1=0;$d1<@{$ad};$d1++){ + print OUT "${${$ad}[$d1]}{chr}\t"; + print OUT "${${$ad}[$d1]}{source}\t"; + print OUT "${${$ad}[$d1]}{type}\t"; + print OUT "${${$ad}[$d1]}{start}\t"; + print OUT "${${$ad}[$d1]}{end}\t"; + print OUT "${${$ad}[$d1]}{score}\t"; + print OUT "${${$ad}[$d1]}{sym}\t"; + print OUT "${${$ad}[$d1]}{phase}\t"; + print OUT "${${$ad}[$d1]}{gid}; "; + print OUT "${${$ad}[$d1]}{tid};\n"; + } +} + +sub Read_GTF{ + my ($file) = @_; + my @gvec; + my @re; + my $begin = 1; + my $pre_tid; + my $pre_gid; + my $i = 0; + my $j = 0; + my $k = 0; + my @temp; + open(IN,$file)||die "open $file error:$!\n"; + while(){ + chomp; + if(/^[0-9a-zA-Z]+/){ + if($begin == 1){ + @temp = split("\t",$_); + $temp[8]=~/(gene_id \"[^\"]+\"); (transcript_id \"[^\"]+\")/; + $pre_tid = $2; + $pre_gid = $1; + + $gvec[$i] = init_gene(); + ${$gvec[$i]}[$j] = init_tran(); + + ${${$gvec[$i]}[$j]}[$k] = + new_sf($temp[0],$temp[1],$temp[2],$temp[3],$temp[4],$temp[5],$temp[6],$temp[7],$1,$2); + $begin = 0; + } + else{ + @temp = split("\t",$_); + $temp[8] =~ /(gene_id \"[^\"]+\"); (transcript_id \"[^\"]+\")/; + + if($1 eq $pre_gid){ + if($2 eq $pre_tid){ + $k++; + ${${$gvec[$i]}[$j]}[$k] = + new_sf($temp[0],$temp[1],$temp[2],$temp[3],$temp[4],$temp[5],$temp[6],$temp[7],$1,$2); + } + else{ + $j++; + ${$gvec[$i]}[$j] = init_tran(); + $k = 0; + ${${$gvec[$i]}[$j]}[$k] = + new_sf($temp[0],$temp[1],$temp[2],$temp[3],$temp[4],$temp[5],$temp[6],$temp[7],$1,$2); + $pre_tid = $2; + } + } + else{ + $i++; + $gvec[$i] = init_gene(); + $j = 0; + ${$gvec[$i]}[$j] = init_tran(); + $k = 0; + ${${$gvec[$i]}[$j]}[$k] = + new_sf($temp[0],$temp[1],$temp[2],$temp[3],$temp[4],$temp[5],$temp[6],$temp[7],$1,$2); + $pre_gid =$1; + $pre_tid = $2; + } + } + } + } + close IN; + $re[0] = \@gvec; + $re[1] = scalar(@gvec); + return \@re; +} + +sub new_sf{ + my ($chr,$src,$type,$start,$end,$score,$sym,$phase,$gid,$tid)=@_; + my %hash = ( + "chr" => $chr, + "source" => $src, + "type" => $type, + "score" => $score, + "gid" => $gid, + "tid" => $tid, + "start" => $start, + "end" => $end, + "sym" => $sym, + "phase" => $phase, + ); + return \%hash; +} + +sub init_gene{ + my @a; + return \@a; +} +sub init_tran{ + my @a; + return \@a; +} +1; +} +1; diff --git a/src/ccov/CCOV.cpp b/src/ccov/CCOV.cpp index d615849..e8e7441 100644 --- a/src/ccov/CCOV.cpp +++ b/src/ccov/CCOV.cpp @@ -138,9 +138,13 @@ int main(int argc, char* argv[]){ //Check coverage cerr <<"Calculate coverage and evenness" <<" ......"< > &mapper, GTF >f){ + int mycount=0; vector::iterator giter=gtf.GeneStructureSequence.begin(); while(giter!=gtf.GeneStructureSequence.end()){ + mycount++; + cerr << "While loop number: " << mycount < Date: Mon, 7 Mar 2022 17:45:13 +0200 Subject: [PATCH 03/28] Quast step now analyses Minimap results --- lib/HUPANunalnCtgSLURM.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/HUPANunalnCtgSLURM.pm b/lib/HUPANunalnCtgSLURM.pm index 303912e..1a384e4 100644 --- a/lib/HUPANunalnCtgSLURM.pm +++ b/lib/HUPANunalnCtgSLURM.pm @@ -140,7 +140,8 @@ foreach my $s (@sample){ $unalign_info_file=$quad.$unalign_info_file; #obtain the filtered coords file within quast dir - $quad.="nucmer_output/"; + $quad.="minimap_output/"; + #$quad.="nucmer_output/"; my $coords_file=""; opendir(ASS,$quad) || die("Error04: cannot open data directory: $quad\n"); my @nucmer_files=readdir(ASS); From b477ec96672d97c79166bb87ceaead4cfcc36ba5 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Tue, 8 Mar 2022 09:40:20 +0200 Subject: [PATCH 04/28] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index f6b758c..3e30733 100644 --- a/README.md +++ b/README.md @@ -162,9 +162,9 @@ hupanSLURM extractSeq 01_assembled 03_candidate 02_aligned * This steps maps the assembled contigs in the candidate folder against the reference and checks the statistics of these contigs using QUAST. * The QUAST results of the candidate contigs are saved in a folder called 04_quastresult. -* /cbio/bin if where the QUAST exectuable is located, which runs a QUAST Singularity container. +* /cbio/projects/015/HUPANdatabases/images/ is where the QUAST exectuable is located, which runs a QUAST Singularity container. ``` -hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/bin/ /cbio/projects/015/HUPANdatabases/ref/ref.fa +hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HUPANdatabases/images/ /cbio/projects/015/HUPANdatabases/ref/ref.fa ``` hupanSLURM assemSta code is found in `/cbio/soft/HUPAN/lib/HUPANassemStaSLURM.pm` @@ -265,9 +265,9 @@ hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/nonrefernce.before.fa 1 * The population directories should all be in the same location and can therefore be accessed using *. * The final non-reference sequences are saved in allpopulations/ ``` -cat */12_finalpangenome/non-redundant.fa > ../allpopulations/11_nonreference/all.nonrefernce.before.fa +cat */12_finalpangenome/non-redundant.fa > ../allpopulations/11_nonreference/all.nonreference.before.fa cd ../allpopulations -hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/all.nonrefernce.before.fa 12_finalpangenome /cbio/bin/ +hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/all.nonreference.before.fa 12_finalpangenome /cbio/bin/ ``` * This will result in the final non-redundant non-reference sequence file in `allpopulations/12_finalpangenome/non-redundant.fa` for all populations combined. * All steps from this point are performed in the `allpopulations` directory. From 357844a9afdbc243e05641262ffbe299f9819227 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Fri, 11 Mar 2022 12:11:15 +0200 Subject: [PATCH 05/28] Create test --- plottingScripts/test | 1 + 1 file changed, 1 insertion(+) create mode 100644 plottingScripts/test diff --git a/plottingScripts/test b/plottingScripts/test new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/plottingScripts/test @@ -0,0 +1 @@ + From 393661aa4a367eafd03e3e04dfca7363431d23b8 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Mon, 14 Mar 2022 08:27:37 +0200 Subject: [PATCH 06/28] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3e30733..4ff9f5d 100644 --- a/README.md +++ b/README.md @@ -299,8 +299,9 @@ hupanSLURM genePre -t 16 13_genepredinput 14_genepred /cbio/projects/008/jess/HU **(15) Merging the novel predictions** * This step merges the novel predictions from the different parts. -* It akes in the directory where all the different parts' results are (14_genepred) and places them into single files in 15_genepredmerge. +* It takes in the directory where all the different parts' results are (14_genepred) and places them into single files in 15_genepredmerge. * /cbio/bin is where the MAKER executable is. +* This step is run interactively and produces output in real time (takes about 10 minutes), so first run `screen` and then use a minimal interactive node: `srun --pty bash` ``` hupanSLURM mergeNovGene 14_genepred/result/ 15_genepredmerge /cbio/bin ``` From 0e87aab43a980b8a97ba1d2f1213914a0fe44968 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Tue, 15 Mar 2022 09:44:12 +0200 Subject: [PATCH 07/28] Updated location of HUPAN library --- README.md | 172 +++++++++++++++++++++++++++--------------------------- 1 file changed, 87 insertions(+), 85 deletions(-) diff --git a/README.md b/README.md index 4ff9f5d..a541d3b 100644 --- a/README.md +++ b/README.md @@ -131,104 +131,104 @@ Notes: **(1) *De novo* assembly of individual genomes** -This step assembles the fastq files of each genome into a whole genome using SGA. The assembled sequences are saved in a directory called 01_assembled. +This step assembles the fastq files of each genome into a whole genome using SGA. The assembled sequences are saved in a directory called `01_assembled`. This step has been changed from the original HUPAN process; a Nextflow pipeline is now used, developed by Gerrit Botha and myself. The Nextflow pipeline repository can be found at: https://github.com/h3abionet/dec-2020-hackathon-stream1/tree/main/assembly **(2) Aligning samples to the reference genome** * This step aligns the assembled genome to the reference genome using the nucmer tool in MUMmer. -* The aligned sequences are saved in a folder called 02_aligned. -* /cbio/bin is the path to the MUMmer, nucmer and show-cords executable files, which all run through a MUMmer Singularity container. +* The aligned sequences are saved in a folder called `02_aligned`. +* `/cbio/bin` is the path to the MUMmer, nucmer and show-cords executable files, which all run through a MUMmer Singularity container. ``` hupanSLURM alignContig -t 16 01_assembled 02_aligned /cbio/bin /cbio/projects/015/HUPANdatabases/ref/ref.fa ``` -* This will result in .delta and .coords files for each sample. -* hupanSLURM alignContig code is found in `/cbio/soft/HUPAN/lib/HUPANrmHighSLURM.pm` +* This will result in `.delta` and `.coords` files for each sample. +* hupanSLURM alignContig code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmHighSLURM.pm` **(3) Extracting contigs with a low similarity to the reference genome** * This step identifies and discards all those contigs with > 95% identity and contig length alignment to the reference genome. -* The sequences with low similarity (and that are potentially non-reference sequences) are saved in a folder called 03_candidate. -* The final argument (02_aligned) is the path to the MUMmer/nucmer results, created in the previous step. +* The sequences with low similarity (and that are potentially non-reference sequences) are saved in a folder called `03_candidate`. +* The final argument (`02_aligned`) is the path to the MUMmer/nucmer results, created in the previous step. * This step is run interactively and produces output in real time, so first run `screen` and then use an interactive node: `srun --nodes=1 --ntasks=1 --mem=50g -t 24:00:00 --pty bash` ``` hupanSLURM extractSeq 01_assembled 03_candidate 02_aligned ``` -* This will result in a .candidate.unaligned.contig file for each sample. -* hupanSLURM extractSeq code is found in `/cbio/soft/HUPAN/lib/HUPANrmHighSLURM.pm` +* This will result in a `.candidate.unaligned.contig` file for each sample. +* hupanSLURM extractSeq code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmHighSLURM.pm` **(4) Assessing the candidate sequences using QUAST** * This steps maps the assembled contigs in the candidate folder against the reference and checks the statistics of these contigs using QUAST. -* The QUAST results of the candidate contigs are saved in a folder called 04_quastresult. -* /cbio/projects/015/HUPANdatabases/images/ is where the QUAST exectuable is located, which runs a QUAST Singularity container. +* The QUAST results of the candidate contigs are saved in a folder called `04_quastresult`. +* `/cbio/projects/015/HUPANdatabases/images/` is where the QUAST exectuable is located, which runs a QUAST Singularity container. ``` hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HUPANdatabases/images/ /cbio/projects/015/HUPANdatabases/ref/ref.fa ``` -hupanSLURM assemSta code is found in `/cbio/soft/HUPAN/lib/HUPANassemStaSLURM.pm` +hupanSLURM assemSta code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANassemStaSLURM.pm` **(5) Collecting unaligned (both fully and partially) contigs** -* This steps collects all unaligned (both fully and partially) contigs from the 03_candidate folder using information from the 04_quastresult folder. -* The final unaligned sequences will be saved in folder called 05_unaligned. -* The HUPAN notes on GitHub say to use -p to specify .contig suffix, but the actual .pm file says to use -s. +* This steps collects all unaligned (both fully and partially) contigs from the 03_candidate folder using information from the `04_quastresult` folder. +* The final unaligned sequences will be saved in folder called `05_unaligned`. +* The HUPAN notes on GitHub say to use `-p` to specify .contig suffix, but the actual .pm file says to use `-s`. ``` hupanSLURM getUnalnCtg -s .contig 03_candidate/data 04_quastresult/data 05_unaligned ``` -This will result in .fully.contig, partially.contig and partially.coords files for each sample. -hupanSLURM getUnalnCtg code is found in `/cbio/soft/HUPAN/lib/HUPANunalnCtgsSLURM.pm` +This will result in `.fully.contig`, `partially.contig` and `partially.coords` files for each sample. +hupanSLURM getUnalnCtg code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANunalnCtgsSLURM.pm` **(6) Merging all the unaligned contigs** -* This step merges all the unaligned contigs in 05_unaligned. -* The resulting files will be saved in the folder 06_mergeunaligned. +* This step merges all the unaligned contigs in `05_unaligned`. +* The resulting files will be saved in the folder `06_mergeunaligned`. * Partially and fully unaligned contigs are still kept separate, and will each result in one file each. ``` hupanSLURM mergeUnalnCtg 05_unaligned/data 06_mergeunaligned ``` This will result in total.fully.fa, total.partilly.coords and total.partilly.fa files with all the merged data. -hupanSLURM mergeUnalnCtg code is found in `/cbio/soft/HUPAN/lib/HUPANunalnCtgsSLURM.pm` +hupanSLURM mergeUnalnCtg code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANunalnCtgsSLURM.pm` **(7) Removing redundancy** * This step removes redundancy (i.e. similar sequences) using CD-HIT. * It does this by forming 'clusters' of similar contigs at a defined identity threshold and choosing the longest contig in that cluster as the representative contig. * The command must be performed twice; once for fully unaligned sequences, and once for partially unaligned sequences. -* They must be run in a separate directory, called 07_rmredundant. The restults will then be stored in directories within this directory. -* The default % identity for clustering using CD-HIT in HUPAN is 90%, but you can change it by using the -c flag, e.g. `-c 0.85` -* /cbio/bin is the location of the cd-hit-est exectuable, which runs a Singularity container. +* They must be run in a separate directory, called `07_rmredundant`. The restults will then be stored in directories within this directory. +* The default % identity for clustering using CD-HIT in HUPAN is 90%, but you can change it by using the `-c` flag, e.g. `-c 0.85` +* `/cbio/bin` is the location of the cd-hit-est exectuable, which runs a Singularity container. ``` mkdir 07_rmredundant && cd 07_rmredundant hupanSLURM rmRedundant cdhitCluster -t 8 ../06_mergeunaligned/total.fully.fa rmredundant.fully /cbio/bin hupanSLURM rmRedundant cdhitCluster -t 8 ../06_mergeunaligned/total.partilly.fa rmredundant.partially /cbio/bin/ ``` -* This will result in cluster_info.txt and non-redundant.fa files each for both fully and partially unaligned sequences. -* hupanSLURM rmRedundant code is found in `/cbio/soft/HUPAN/lib/HUPANrmRdtSLURM.pm` +* This will result in `cluster_info.txt` and `non-redundant.fa` files each for both fully and partially unaligned sequences. +* hupanSLURM rmRedundant code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmRdtSLURM.pm` **(8) Identifying contamination in the unaligned sequences** * This step identifies contamination by comparing all unaligned sequences to the BLAST nucleotide database. * The database has been previously downloaded and set up according to HUPAN GitHub instructions (found above). -* The aligned results will be saved in a directory called 08_blastresult. Within this directory, there will be a rmredundant.fully and a rmredundant.partially directory. -* /cbio/bin is where the BLAST executable file is found. +* The aligned results will be saved in a directory called `08_blastresult`. Within this directory, there will be a `rmredundant.fully` and a `rmredundant.partially` directory. +* `/cbio/bin` is where the BLAST executable file is found. ``` hupanSLURM blastAlign blast -t 16 07_rmredundant 08_blastresult /cbio/projects/015/HUPANdatabases/blastindex/data/blastdb /cbio/bin ``` -* This will result in non-redundan.blast files. -* hupanSLURM blastAlign code is found in `/cbio/soft/HUPAN/lib/HUPANblastAlignSLURM.pm` +* This will result in `non-redundan.blast` files. +* hupanSLURM blastAlign code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANblastAlignSLURM.pm` **(9) Obtaining the taxonomic classifications of the sequences** * This steps looks at all the BLAST hits and classifies them into their correct taxonomies (if there are any). * It uses two databases downloaded from NCBI: a taxonomy database, and a database that converts accession numbers to taxonomic IDs. Both have already been downloaded and set up (instructuions found above). * The command has to be run twice, once each for partially and fully unaligned sequences. -* Each command will create its own directory; 09.1_taxclassfully for fully unaligned reads and 09.2_taxclasspartially for partially unaligned reads. +* Each command will create its own directory; `09.1_taxclassfully` for fully unaligned reads and `09.2_taxclasspartially` for partially unaligned reads. ``` hupanSLURM getTaxClass 08_blastresult/data/rmredundant.fully/non-redundan.blast /cbio/projects/015/HUPANdatabases/taxonomyinfo 09.1_taxclassfully hupanSLURM getTaxClass 08_blastresult/data/rmredundant.partially/non-redundan.blast /cbio/projects/015/HUPANdatabases/taxonomyinfo 09.2_taxclasspartially ``` -* hupanSLURM getTaxClass code is found in `/cbio/soft/HUPAN/lib/HUPANgetTaxClassSLURM.pm` +* hupanSLURM getTaxClass code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgetTaxClassSLURM.pm` **(10) Removing contaminating sequences** @@ -241,20 +241,20 @@ hupanSLURM getTaxClass 08_blastresult/data/rmredundant.partially/non-redundan.bl hupanSLURM rmCtm -i 60 07_rmredundant/rmredundant.fully/non-redundant.fa 08_blastresult/data/rmredundant.fully/non-redundan.blast 09.1_taxclassfully/accession.name 10.1_rmctmfully hupanSLURM rmCtm -i 60 07_rmredundant/rmredundant.partially/non-redundant.fa 08_blastresult/data/rmredundant.partially/non-redundan.blast 09.2_taxclasspartially/accession.name 10.2_rmctmpartially ``` -* hupanSLURM rmCtm code is found in `/cbio/soft/HUPAN/lib/HUPANrmContaminateSLURM.pm` +* hupanSLURM rmCtm code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmContaminateSLURM.pm` **(11) Combining fully and partially unaligned reads** * This steps removes redundancy again by merging the final fully and partially unaligned sequences, again using CD-HIT. * A directory must first be made and then the fully and partially unaligned sequences combined and moved into this directory. This is done in the first command below. -* This combined file is then run through CD-HIT to remove redundancy (at 90% identity) and the final non-redundant non-reference contigs are saved in 12_finalpangenome. -* /cbio/bin is the location of the CD-HIT executable. +* This combined file is then run through CD-HIT to remove redundancy (at 90% identity) and the final non-redundant non-reference contigs are saved in `12_finalpangenome`. +* `/cbio/bin` is the location of the CD-HIT executable. ``` mkdir 11_nonreference && cat 10.1_rmctmfully/novel_sequence.fa 10.2_rmctmpartially/novel_sequence.fa > 11_nonreference/nonrefernce.before.fa hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/nonrefernce.before.fa 12_finalpangenome /cbio/bin/ ``` -* This will result in a tmp directory and cluster_info.txt and non-redundant.fa files. -* hupanSLURM rmRedundant code is found in `/cbio/soft/HUPAN/lib/HUPANrmRdtSLURM.pm` +* This will result in a `tmp` directory and `cluster_info.txt` and `non-redundant.fa` files. +* hupanSLURM rmRedundant code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmRdtSLURM.pm` **(12) Merging the different populations** @@ -263,73 +263,73 @@ hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/nonrefernce.before.fa 1 **By doing this, we are ending up with the same sequences we would have had if we had run all the populations together, but now we have the population-specific information separated and can easily perform downstream or upstream analysis on population differences.** * To do this, use `cat` to combine all the sequences into one file, and then use CD-HIT to remove redundancy at 90%. * The population directories should all be in the same location and can therefore be accessed using *. -* The final non-reference sequences are saved in allpopulations/ +* The final non-reference sequences are saved in `allpopulations/` ``` cat */12_finalpangenome/non-redundant.fa > ../allpopulations/11_nonreference/all.nonreference.before.fa cd ../allpopulations hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/all.nonreference.before.fa 12_finalpangenome /cbio/bin/ ``` * This will result in the final non-redundant non-reference sequence file in `allpopulations/12_finalpangenome/non-redundant.fa` for all populations combined. -* All steps from this point are performed in the `allpopulations` directory. +* All steps from this point are performed in the `allpopulations/` directory. **(13) Splitting the sequences into smaller files** * This step splits the non-redundant non-reference sequences into smaller files so that MAKER can handle them easier and quicker. * It takes the fasta file and saves it as smaller files in the second directory given. -* It splits the fasta file into files that contain ~6000 contigs. -* The output directory is 13_genepredinput. +* It splits the fasta file into files that contain roughly 2 Mbp, set using the `-m 2000000` flag +* The output directory is `13_genepredinput`. ``` -hupanSLURM splitSeq 12_finalpangenome/non-redundant.fa 13_genepredinput +hupanSLURM splitSeq -m 2000000 12_finalpangenome/non-redundant.fa 13_genepredinput ``` -* This will result in a number of part*.fa files, each consisting of around 6000 sequences -* The number of files will depend on how many sequences were in the non-redundant.fa file. -* hupanSLURM splitSeq code is found in `/cbio/soft/HUPAN/lib/HUPANsplitSeqSLURM.pm` +* This will result in a number of `part*.fa` files. +* The number of files will depend on how many sequences were in the `non-redundant.fa` file. +* hupanSLURM splitSeq code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANsplitSeqSLURM.pm` **(14) Predicting genes from the non-reference sequences** * This step takes the split up non-reference sequence files and inputs them into MAKER. * The config is the MAKER configuration file where we have specified all of the variables and datasets to use. A copy of this config file can be found in this repository. -* /cbio/bin is the location of the MAKER executable, which runs a MAKER Singularity container. +* `/cbio/bin` is the location of the MAKER executable, which runs a MAKER Singularity container. ``` hupanSLURM genePre -t 16 13_genepredinput 14_genepred /cbio/projects/008/jess/HUPANrun/AfricanPanGenome/config /cbio/bin ``` -* This will result in various MAKER predictions for each part*.fa file. -* hupanSLURM genePre code is found in `/cbio/soft/HUPAN/lib/HUPANgenePreSLURM.pm` +* This will result in various MAKER predictions for each `part*.fa` file. +* hupanSLURM genePre code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgenePreSLURM.pm` **(15) Merging the novel predictions** * This step merges the novel predictions from the different parts. -* It takes in the directory where all the different parts' results are (14_genepred) and places them into single files in 15_genepredmerge. -* /cbio/bin is where the MAKER executable is. +* It takes in the directory where all the different parts' results are (`14_genepred`) and places them into single files in `15_genepredmerge`. +* `/cbio/bin` is where the MAKER executable is. * This step is run interactively and produces output in real time (takes about 10 minutes), so first run `screen` and then use a minimal interactive node: `srun --pty bash` ``` hupanSLURM mergeNovGene 14_genepred/result/ 15_genepredmerge /cbio/bin ``` -* This will result in all.maker.map, combine.all.maker.gff, combine.all.maker.proteins.fasta and combine.all.maker.transcripts.fasta files. -* hupanSLURM mergeNovGene code is found in `/cbio/soft/HUPAN/lib/HUPANmergeNovGene.pm` +* This will result in `all.maker.map`, `combine.all.maker.gff`, `combine.all.maker.proteins.fasta` and `combine.all.maker.transcripts.fasta` files. +* hupanSLURM mergeNovGene code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANmergeNovGene.pm` **(16) Filtering the gene predicitons** * This step filters and refines the novel predicted genes based on HUPAN specifications. These specifications can be found in the HUPAN paper supplementary methods. -* The first command copies the non-redundant.fa sequence file from 12_finalpangenome to the 15_genepredmerge directory, because the script needs it to work. Call it novel.fa. -* The ref/ directory contains exactly what the HUPAN script looks for with the exact names, i.e. ref.fa and ref.transcripts.fa (explained above). +* The first command copies the `non-redundant.fa` sequence file from `12_finalpangenome` to the `15_genepredmerge` directory, because the script needs it to work. Call it `novel.fa`. +* The `ref/` directory contains exactly what the HUPAN script looks for with the exact names, i.e. `ref.fa` and `ref.transcripts.fa` (explained above). * The last three inputs are (in order) the locations of the BLAST, CD-HIT and RepeatMasker executables respectively. ``` cp 12_finalpangenome/non-redundant.fa 15_genepredmerge/novel.fa hupanSLURM filterNovGene -t 16 15_genepredmerge 16_genepredfilter /cbio/projects/015/HUPANdatabases/ref /cbio/bin/ /cbio/bin/ /cbio/bin/ ``` -* hupanSLURM filterNovGene code is found in `/cbio/soft/HUPAN/lib/HUPANfilterNovGeneSLURM.pm` +* hupanSLURM filterNovGene code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANfilterNovGeneSLURM.pm` **(17) Assembling the pan-genome** * This step has does two things. First: - * It takes in the human reference annotation file in ref/ref.genes.fa and retains only the longest transcript of each annotation while discarding others, like mRNA, lncRNA, etc. - * The -f flag just tells the script that the file is in gtf format, not gff. - * It saves the annotations in a file called ref.genes-ptpg.gtf, found in the /cbio/projects/015/HUPANdatabases/ref directory. + * It takes in the human reference annotation file in `ref/ref.genes.fa` and retains only the longest transcript of each annotation while discarding others, like mRNA, lncRNA, etc. + * The `-f` flag just tells the script that the file is in gtf format, not gff. + * It saves the annotations in a file called `ref.genes-ptpg.gtf`, found in the `/cbio/projects/015/HUPANdatabases/ref` directory. * The annotation file was downloaded from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.chr_patch_hapl_scaff.annotation.gtf.gz (release 38). - * The annotation file downloaded must be later than release 21, otherwise the HUPAN script won't work as it will be in a different format (format changed after release 21). - * However, you also have to remove any annotations from patch/alt/decoy/unplaced contigs! So remove from the file all lines after "chrM" (mitochondrial DNA) annotations. I have not shown this step below, as the exact line numbers may be different. - * So essentially, run the pTpG script on the annotation file, and then remove the extra annotations and save the final working file as ref.genes-ptpg-primaryseqs.gtf. + * The annotation file downloaded MUST be later than release 21, otherwise the HUPAN script won't work as it will be in a different format (format changed after release 21). + * However, you also have to remove any annotations from patch/alt/decoy/unplaced/mitochondrial DNA contigs, as the HUPAN pipeline seems to be unable to recognise them. So remove from the annotation file all lines after "chrY" annotations. I have not shown this step below, as the exact line numbers may be different. + * In summary: run the `pTpG` script on the annotation file, and then remove the extra annotations and save the final working file as `ref.genes-ptpg-primaryseqs.gtf`. * Then secondly, we combine this annotation file and the novel sequence annotation (from step 16) into one annotation file * You must first convert the novel annotation file into GTF format too, or otherwise start with GFF format for the reference annotation. * Both steps done in real time (interactively) so use `screen` and then start an interactive node with extra memory: `srun --mem=15g --pty bash` @@ -339,53 +339,53 @@ hupanSLURM pTpG -f /cbio/projects/015/HUPANdatabases/ref/ref.genes.gtf /cbio/pro # insert step to convert the Final.gff file to GTF format. mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primaryseqs.gtf 16_genepredfilter/data/Final/Final.gtf > 17_pan/pan.gtf ``` -* hupanSLURM pTpG code is found in `/cbio/soft/HUPAN/lib/HUPANpTpGSLURM.pm` +* hupanSLURM pTpG code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANpTpGSLURM.pm` **(18) Aligning the samples to the pan-genome** * This step does three things: - * First, it combines the novel sequences with the human reference sequences into one file called pan.fa. This is the final pan-genome file. - * It then uses the bowtie2-build function to build a Bowtie index from the pan-genome sequences. - * This is done interactively and requires a lot of memory, so a `screen` session and an interactive node is required for the second command: `srun --mem=50g --time=24:00:00 --pty bash` -* Finally, it then aligns all the fastq files (of each genome) to the pan-genome file using Bowtie 2. The fastq files of all samples are found in 0_fastq. -* The -f flag specifies Bowtie2 (not BWA), and the -s and -k flags specify the naming convention of the fastq files given (e.g. LZP0B_R1.fastq.gz) -* 18_map2pan is the output directory. -* /cbio/projects/015/HUPANdatabases/images/ is where I have stored the Bowtie 2 Singularity container. + * First, it combines the novel sequences with the human reference sequences into one file called `pan.fa`. This is the final pan-genome file. + * It then uses the `bowtie2-build` function to build a Bowtie index from the pan-genome sequences. + * This is done interactively and requires a lot of memory, so a `screen` session and an interactive node are required for the second command: `srun --mem=50g --time=24:00:00 --pty bash` +* Finally, it then aligns all the fastq files (of each genome) to the pan-genome file using Bowtie 2. The fastq files of all samples are found in `0_fastq`. +* The `-f` flag specifies Bowtie2 (not BWA), and the `-s` and `-k` flags specify the naming convention of the fastq files given (e.g. `LZP0B_R1.fastq.gz`) +* `18_map2pan` is the output directory. +* `/cbio/projects/015/HUPANdatabases/images/` is where I have stored the Bowtie 2 Singularity container. ``` cat /cbio/projects/015/HUPANdatabases/ref/ref.fa 12_finalpangenome/non-redundant.fa > 17_pan/pan.fa cd 17_pan && /cbio/projects/015/HUPANdatabases/images/bowtie2-build pan.fa pan && cd .. hupanSLURM alignRead -f bowtie2 -t 8 -s .fastq.gz -k _R 0_fastq 18_map2pan /cbio/projects/015/HUPANdatabases/images/ 17_pan/pan ``` -* The final command will result in a .sam file for each fastq file (genome/individual) given. -* hupanSLURM alignRead code is found in `/cbio/soft/HUPAN/lib/HUPANmapSLURM.pm` +* The final command will result in a `.sam file` for each fastq file (genome/individual) given. +* hupanSLURM alignRead code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANmapSLURM.pm` **(19) Converting to SAM format** -* This step uses Samtools to convert the .sam to .bam and then sort and index the .bam files. -* It takes in the .sam files in the 18_map2pan directory and outputs the sorted and indexed .bam files to the 19_panBam directory. -* /cbio/bin is where the Samtools executable is found. +* This step uses Samtools to convert the `.sam` files to `.bam` format and then sort and index the `.bam` files. +* It takes in the `.sam` files in the `18_map2pan` directory and outputs the sorted and indexed `.bam` files to the `19_panBam` directory. +* `/cbio/bin` is where the Samtools executable is found. ``` hupanSLURM sam2bam -t 8 18_map2pan/data 19_panBam /cbio/bin ``` -* This will result in a .bam and .bai file for each fastq file (genome/individual) given. -* hupanSLURM sam2bam code is found in `/cbio/soft/HUPAN/lib/HUPANsamToBamSLURM.pm` +* This will result in a `.bam` and `.bai` file for each fastq file (genome/individual) given. +* hupanSLURM sam2bam code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANsamToBamSLURM.pm` **(20) Calculating gene coverage** * This step calculates the coverage of each gene or CDS in all of the genomes used. -* It does this by looking at the alignment information in the indexed and sorted .bam files from the previous step and identifying whether these alignments fall within the annotations in the pan.gtf file. -* The results will be output to the 20_geneCov directory. +* It does this by looking at the alignment information in the indexed and sorted `.bam` files from the previous step and identifying whether these alignments fall within the annotations in the `pan.gtf` file. +* The results will be output to the `20_geneCov` directory. ``` hupanSLURM geneCov -t 8 19_panBam/data 20_geneCov/ 17_pan/pan.gtf ``` -* This will result in a .sta file for each genome. -* hupanSLURM geneCov code is found in `/cbio/soft/HUPAN/lib/HUPANgeneCovSLURM.pm` +* This will result in a `.sta` file for each genome. +* hupanSLURM geneCov code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneCovSLURM.pm` **(21) Determing gene presence-absence variance profile** * This steps checks whether a gene is present or absent (based on a defined coverage threshold) for each sample. -* The gene coverage information from the 20_geneCov directory is first combined into two files, one recording gene coverage and one recording CDS coverage. - * The first input is the prefix you want to use for the merged file, and the second input is that data directory where the .sta files are. +* The gene coverage information from the `20_geneCov` directory is first combined into two files, one recording gene coverage and one recording CDS coverage. + * The first input is the prefix you want to use for the merged file, and the second input is that data directory where the `.sta` files are. * The final HUPAN command takes in the two files outputted from the previous command and creates the gene presence-absence variance profile. * It does this by checking the gene or CDS coverage at a certain threshold. HUPAN sets theirs at 95% gene coverage. * For this command, the two integer values are (in order) the minimum gene coverage and the minimum CDS coverage. @@ -393,7 +393,9 @@ hupanSLURM geneCov -t 8 19_panBam/data 20_geneCov/ 17_pan/pan.gtf cd 20_geneCov && hupanSLURM mergeGeneCov geneCovmerged 20_geneCov/data mkdir 21_geneExist && hupanSLURM geneExist 20_geneCov/summary_gene.cov 20_geneCov/summary_cds.cov 0 0.95 > 21_geneExist/gene.exist ``` -* The first command will result in geneCovmergedgene.cov and geneCovmergedcds.cov files. -* hupanSLURM mergeGeneCov code is found in `/cbio/soft/HUPAN/lib/HUPANgeneCovSLURM.pm` -* The second command will result in the gene.exist file. -* hupanSLURM geneExist code is found in `/cbio/soft/HUPAN/lib/HUPANgeneExistSLURM.pm` +* The first command will result in `geneCovmergedgene.cov` and `geneCovmergedcds.cov` files. +* hupanSLURM mergeGeneCov code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneCovSLURM.pm` +* The second command will result in the `gene.exist file`. +* hupanSLURM geneExist code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneExistSLURM.pm` + +And now you're finally done! From 115047f56d153fb02f2034e55334d2ac5066872e Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Tue, 15 Mar 2022 13:45:42 +0200 Subject: [PATCH 08/28] Updated name of 0_fastq directory --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index a541d3b..48bdbb5 100644 --- a/README.md +++ b/README.md @@ -347,14 +347,14 @@ mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primary * First, it combines the novel sequences with the human reference sequences into one file called `pan.fa`. This is the final pan-genome file. * It then uses the `bowtie2-build` function to build a Bowtie index from the pan-genome sequences. * This is done interactively and requires a lot of memory, so a `screen` session and an interactive node are required for the second command: `srun --mem=50g --time=24:00:00 --pty bash` -* Finally, it then aligns all the fastq files (of each genome) to the pan-genome file using Bowtie 2. The fastq files of all samples are found in `0_fastq`. +* Finally, it then aligns all the fastq files (of each genome) to the pan-genome file using Bowtie 2. The fastq files of all samples are found in `00_fastq`. * The `-f` flag specifies Bowtie2 (not BWA), and the `-s` and `-k` flags specify the naming convention of the fastq files given (e.g. `LZP0B_R1.fastq.gz`) * `18_map2pan` is the output directory. * `/cbio/projects/015/HUPANdatabases/images/` is where I have stored the Bowtie 2 Singularity container. ``` cat /cbio/projects/015/HUPANdatabases/ref/ref.fa 12_finalpangenome/non-redundant.fa > 17_pan/pan.fa cd 17_pan && /cbio/projects/015/HUPANdatabases/images/bowtie2-build pan.fa pan && cd .. -hupanSLURM alignRead -f bowtie2 -t 8 -s .fastq.gz -k _R 0_fastq 18_map2pan /cbio/projects/015/HUPANdatabases/images/ 17_pan/pan +hupanSLURM alignRead -f bowtie2 -t 8 -s .fastq.gz -k _R 00_fastq 18_map2pan /cbio/projects/015/HUPANdatabases/images/ 17_pan/pan ``` * The final command will result in a `.sam file` for each fastq file (genome/individual) given. * hupanSLURM alignRead code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANmapSLURM.pm` From dd2fee1dd688800a13425b6440ee7203560e0cd8 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Wed, 23 Mar 2022 10:06:37 +0200 Subject: [PATCH 09/28] Fixed hupanSLURM geneExist command --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 48bdbb5..8a26eaf 100644 --- a/README.md +++ b/README.md @@ -390,7 +390,7 @@ hupanSLURM geneCov -t 8 19_panBam/data 20_geneCov/ 17_pan/pan.gtf * It does this by checking the gene or CDS coverage at a certain threshold. HUPAN sets theirs at 95% gene coverage. * For this command, the two integer values are (in order) the minimum gene coverage and the minimum CDS coverage. ``` -cd 20_geneCov && hupanSLURM mergeGeneCov geneCovmerged 20_geneCov/data +cd 20_geneCov && hupanSLURM mergeGeneCov geneCovmerged data mkdir 21_geneExist && hupanSLURM geneExist 20_geneCov/summary_gene.cov 20_geneCov/summary_cds.cov 0 0.95 > 21_geneExist/gene.exist ``` * The first command will result in `geneCovmergedgene.cov` and `geneCovmergedcds.cov` files. From 3bb0ef0e7932903e9dd69fc9a8caf2c6a6f3318c Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Wed, 23 Mar 2022 10:10:09 +0200 Subject: [PATCH 10/28] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8a26eaf..63ff8d6 100644 --- a/README.md +++ b/README.md @@ -390,8 +390,8 @@ hupanSLURM geneCov -t 8 19_panBam/data 20_geneCov/ 17_pan/pan.gtf * It does this by checking the gene or CDS coverage at a certain threshold. HUPAN sets theirs at 95% gene coverage. * For this command, the two integer values are (in order) the minimum gene coverage and the minimum CDS coverage. ``` -cd 20_geneCov && hupanSLURM mergeGeneCov geneCovmerged data -mkdir 21_geneExist && hupanSLURM geneExist 20_geneCov/summary_gene.cov 20_geneCov/summary_cds.cov 0 0.95 > 21_geneExist/gene.exist +cd 20_geneCov && hupanSLURM mergeGeneCov summary_ data && cd .. +mkdir 21_geneExist && hupanSLURM geneExist 20_geneCov/summary_gene.cov 20_geneCov/summary_cds.cov 0 0.95 > 21_geneExist/cds95.gene.exist ``` * The first command will result in `geneCovmergedgene.cov` and `geneCovmergedcds.cov` files. * hupanSLURM mergeGeneCov code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneCovSLURM.pm` From 81b44fe6df3c5856023d2b8a5b097f16215dcd7a Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Tue, 5 Apr 2022 09:47:20 +0200 Subject: [PATCH 11/28] Added descriptions of simulation functions --- README.md | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/README.md b/README.md index 63ff8d6..b2c0109 100644 --- a/README.md +++ b/README.md @@ -399,3 +399,29 @@ mkdir 21_geneExist && hupanSLURM geneExist 20_geneCov/summary_gene.cov 20_geneCo * hupanSLURM geneExist code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneExistSLURM.pm` And now you're finally done! + +**Performing simulations using the HUPAN suite** + +* The HUPAN pipelines offers two simulation outputs on your data: + * The `sim` function simulates the size of the core and pan-genomes from the gene presence-absence data generated in step 21. + * The `simSeq` function simulates and plots the total amount of novel sequence as more individuals are added. + +* For the `sim` function: + * A `screen` session and a minimum interactive node are required: `srun --pty bash` + * You must choose whichever `.gene.exist` file is most apprpropriate for analysis of the pan-genome. Here, gene coverage of 95% is chosen. +``` +mkdir 22_simulations +hupanSLURM sim 21_geneExist/gene95.gene.exist 22_simulations/PAV +``` +* This will result in a `sim_out.txt` file and a `sim_out.txt_PAV_plot.pdf` file with the simulated data and plots in them. + +* For the `simSeq` function: + * The first command performs the simulation on the sample-specific unaligned data in `05_unaligned`. + * `/cbio/bin` is the location of the CD-HIT executable which is used for the simulation. + * This simulation will take a few days to run depending on the number of samples. + * The second command just plots the result and is interactive, so a `screen` session and a minimum interactive node are required: `srun --pty bash` +``` +hupanSLURM simSeq simNovelSeq -t 8 05_unaligned/data/ 22_simulations/novelSeqs /cbio/bin +hupanSLURM simSeq plotNovelSeq 22_simulations/novelSeqs/ outputPlot +``` +* This will result in a `simNovelSeq.pdf` file with the simulated plot. From 72bbc9331e71ef93627d79e3a728d166e978aa5d Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:25:09 +0200 Subject: [PATCH 12/28] Rename plottingScripts/test to dataAnalysis/JupyterNotebooks/test --- {plottingScripts => dataAnalysis/JupyterNotebooks}/test | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {plottingScripts => dataAnalysis/JupyterNotebooks}/test (100%) diff --git a/plottingScripts/test b/dataAnalysis/JupyterNotebooks/test similarity index 100% rename from plottingScripts/test rename to dataAnalysis/JupyterNotebooks/test From c610e2927c98a4c7b71ffa2f8e7ee2fce836eb18 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:25:30 +0200 Subject: [PATCH 13/28] Create temp --- dataAnalysis/multiQC/temp | 1 + 1 file changed, 1 insertion(+) create mode 100644 dataAnalysis/multiQC/temp diff --git a/dataAnalysis/multiQC/temp b/dataAnalysis/multiQC/temp new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/dataAnalysis/multiQC/temp @@ -0,0 +1 @@ + From b1bd1b064ddb755d8b1edb7498875ba788f98abb Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:26:54 +0200 Subject: [PATCH 14/28] Create temp --- dataAnalysis/multiQC/startingDataset/temp | 1 + 1 file changed, 1 insertion(+) create mode 100644 dataAnalysis/multiQC/startingDataset/temp diff --git a/dataAnalysis/multiQC/startingDataset/temp b/dataAnalysis/multiQC/startingDataset/temp new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/dataAnalysis/multiQC/startingDataset/temp @@ -0,0 +1 @@ + From fdd43a16acc55036f5853555813e88fbfc905c80 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:27:09 +0200 Subject: [PATCH 15/28] Rename dataAnalysis/multiQC/temp to dataAnalysis/multiQC/finalDataset/temp --- dataAnalysis/multiQC/{ => finalDataset}/temp | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename dataAnalysis/multiQC/{ => finalDataset}/temp (100%) diff --git a/dataAnalysis/multiQC/temp b/dataAnalysis/multiQC/finalDataset/temp similarity index 100% rename from dataAnalysis/multiQC/temp rename to dataAnalysis/multiQC/finalDataset/temp From 909ad84a03ab965571fbede213debfccf547e038 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:28:41 +0200 Subject: [PATCH 16/28] Added MultiQC files for starting dataset --- .../startingDataset/Bantumultiqc_report.html | 5290 +++++++++++++++ .../startingDataset/CARFmultiqc_report.html | 5830 +++++++++++++++++ .../startingDataset/CWNCmultiqc_report.html | 5290 +++++++++++++++ .../startingDataset/EAAAmultiqc_report.html | 5290 +++++++++++++++ .../startingDataset/EANSmultiqc_report.html | 5248 +++++++++++++++ .../startingDataset/FWNCmultiqc_report.html | 5290 +++++++++++++++ .../KhoeSanmultiqc_report.html | 5248 +++++++++++++++ 7 files changed, 37486 insertions(+) create mode 100644 dataAnalysis/multiQC/startingDataset/Bantumultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/CARFmultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/CWNCmultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/EAAAmultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/EANSmultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/FWNCmultiqc_report.html create mode 100644 dataAnalysis/multiQC/startingDataset/KhoeSanmultiqc_report.html diff --git a/dataAnalysis/multiQC/startingDataset/Bantumultiqc_report.html b/dataAnalysis/multiQC/startingDataset/Bantumultiqc_report.html new file mode 100644 index 0000000..9f5fceb --- /dev/null +++ b/dataAnalysis/multiQC/startingDataset/Bantumultiqc_report.html @@ -0,0 +1,5290 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        + Bioinformatics (2016)
        + doi: 10.1093/bioinformatics/btw354
        + PMID: 27312411 +
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        + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

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        Report + + generated on 2022-03-30, 11:19 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/BantuNC

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        +

        General Statistics

        + + + + + + + + + + Showing 37/37 rows and 2/2 columns. + +
        +
        + +
        Sample NameN50 (Kbp)Length (Mbp)
        LP6005441_DNA_B02.assemble_contigs
        0.9Kbp
        1860.1Mbp
        LP6005441_DNA_F01.assemble_contigs
        1.1Kbp
        1957.2Mbp
        LP6005443_DNA_A01.assemble_contigs
        1.3Kbp
        2182.1Mbp
        LP6005443_DNA_E02.assemble_contigs
        1.2Kbp
        2111.6Mbp
        LP6005443_DNA_F02.assemble_contigs
        1.0Kbp
        1763.6Mbp
        LP6005443_DNA_G02.assemble_contigs
        1.1Kbp
        2006.5Mbp
        NA19028.assemble_contigs
        8.0Kbp
        2719.7Mbp
        NA19038.assemble_contigs
        8.2Kbp
        2703.8Mbp
        NA19309.assemble_contigs
        8.4Kbp
        2751.0Mbp
        NA19317.assemble_contigs
        8.4Kbp
        2721.0Mbp
        NA19318.assemble_contigs
        11.0Kbp
        2749.5Mbp
        NA19328.assemble_contigs
        12.3Kbp
        2729.4Mbp
        NA19332.assemble_contigs
        8.5Kbp
        2706.5Mbp
        NA19350.assemble_contigs
        7.8Kbp
        2720.1Mbp
        NA19372.assemble_contigs
        9.8Kbp
        2749.7Mbp
        NA19380.assemble_contigs
        7.9Kbp
        2719.0Mbp
        NA19385.assemble_contigs
        8.1Kbp
        2721.1Mbp
        NA19434.assemble_contigs
        9.9Kbp
        2732.8Mbp
        NA19448.assemble_contigs
        9.5Kbp
        2750.4Mbp
        NA19461.assemble_contigs
        9.8Kbp
        2751.1Mbp
        NA19463.assemble_contigs
        8.2Kbp
        2708.0Mbp
        NA19467.assemble_contigs
        9.7Kbp
        2736.1Mbp
        NA19471.assemble_contigs
        9.5Kbp
        2737.2Mbp
        NA19473.assemble_contigs
        9.2Kbp
        2737.4Mbp
        SAMEA2580844.assemble_contigs
        6.1Kbp
        2716.4Mbp
        SAMEA2580845.assemble_contigs
        5.6Kbp
        2709.8Mbp
        SAMEA2580848.assemble_contigs
        5.8Kbp
        2712.7Mbp
        SAMEA2580849.assemble_contigs
        9.5Kbp
        2730.6Mbp
        SAMEA2580852.assemble_contigs
        5.8Kbp
        2712.1Mbp
        SAMEA2580853.assemble_contigs
        5.7Kbp
        2712.8Mbp
        SAMEA2580854.assemble_contigs
        5.9Kbp
        2713.3Mbp
        SAMEA2580855.assemble_contigs
        6.0Kbp
        2715.6Mbp
        SAMEA2580856.assemble_contigs
        5.7Kbp
        2716.2Mbp
        SAMEA2580858.assemble_contigs
        2.0Kbp
        2522.0Mbp
        SAMEA2580859.assemble_contigs
        3.9Kbp
        2691.3Mbp
        SAMEA2580861.assemble_contigs
        2.1Kbp
        2548.3Mbp
        SAMEA2580862.assemble_contigs
        2.0Kbp
        2506.8Mbp
        + + +
        + + + + + + +
        +

        QUAST

        +

        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

        + + + + +
        + +

        + Assembly Statistics + +

        + + + + +
        + + + + + + + + + Showing 37/37 rows and 10/10 columns. + +
        +
        + +
        Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
        LP6005441_DNA_B02.assemble_contigs
        0.9Kbp
        0.7Kbp
        674.3K
        1259607.0K
        12.1Kbp
        1860.1Mbp
        965.0
        77.74
        12.11
        59.4%
        LP6005441_DNA_F01.assemble_contigs
        1.1Kbp
        0.7Kbp
        600.4K
        1159419.0K
        11.9Kbp
        1957.2Mbp
        1030.0
        82.73
        13.15
        62.5%
        LP6005443_DNA_A01.assemble_contigs
        1.3Kbp
        0.8Kbp
        512.1K
        1043404.0K
        20.6Kbp
        2182.1Mbp
        1279.0
        85.30
        13.89
        69.7%
        LP6005443_DNA_E02.assemble_contigs
        1.2Kbp
        0.8Kbp
        544.7K
        1088768.0K
        23.9Kbp
        2111.6Mbp
        1209.0
        85.25
        14.03
        67.4%
        LP6005443_DNA_F02.assemble_contigs
        1.0Kbp
        0.7Kbp
        611.2K
        1155130.0K
        27.8Kbp
        1763.6Mbp
        817.0
        80.13
        12.66
        56.4%
        LP6005443_DNA_G02.assemble_contigs
        1.1Kbp
        0.8Kbp
        570.5K
        1120871.0K
        16.6Kbp
        2006.5Mbp
        973.0
        85.70
        13.81
        64.1%
        NA19028.assemble_contigs
        8.0Kbp
        4.1Kbp
        97.7K
        214795.0K
        113.8Kbp
        2719.7Mbp
        1547.0
        107.83
        21.03
        88.3%
        NA19038.assemble_contigs
        8.2Kbp
        4.2Kbp
        95.3K
        209954.0K
        118.3Kbp
        2703.8Mbp
        1474.0
        107.51
        21.06
        87.8%
        NA19309.assemble_contigs
        8.4Kbp
        4.3Kbp
        93.7K
        206766.0K
        115.6Kbp
        2751.0Mbp
        1912.0
        110.33
        24.37
        89.0%
        NA19317.assemble_contigs
        8.4Kbp
        4.3Kbp
        93.0K
        205026.0K
        106.1Kbp
        2721.0Mbp
        1600.0
        107.81
        21.14
        88.4%
        NA19318.assemble_contigs
        11.0Kbp
        5.7Kbp
        73.0K
        159601.0K
        129.2Kbp
        2749.5Mbp
        1901.0
        110.76
        25.07
        89.2%
        NA19328.assemble_contigs
        12.3Kbp
        6.3Kbp
        64.3K
        141222.0K
        143.3Kbp
        2729.4Mbp
        1833.0
        111.62
        24.98
        88.6%
        NA19332.assemble_contigs
        8.5Kbp
        4.4Kbp
        92.4K
        203310.0K
        102.1Kbp
        2706.5Mbp
        1610.0
        107.74
        21.15
        87.9%
        NA19350.assemble_contigs
        7.8Kbp
        4.0Kbp
        100.2K
        220742.0K
        95.2Kbp
        2720.1Mbp
        1580.0
        107.41
        21.03
        88.3%
        NA19372.assemble_contigs
        9.8Kbp
        5.0Kbp
        81.2K
        178868.0K
        151.6Kbp
        2749.7Mbp
        1896.0
        111.22
        24.84
        89.1%
        NA19380.assemble_contigs
        7.9Kbp
        4.1Kbp
        99.1K
        218008.0K
        100.3Kbp
        2719.0Mbp
        1522.0
        107.32
        21.02
        88.2%
        NA19385.assemble_contigs
        8.1Kbp
        4.2Kbp
        97.0K
        213510.0K
        129.6Kbp
        2721.1Mbp
        1571.0
        107.94
        21.15
        88.3%
        NA19434.assemble_contigs
        9.9Kbp
        5.1Kbp
        80.3K
        176521.0K
        118.9Kbp
        2732.8Mbp
        1785.0
        109.77
        24.53
        88.5%
        NA19448.assemble_contigs
        9.5Kbp
        4.9Kbp
        83.2K
        183640.0K
        132.2Kbp
        2750.4Mbp
        1947.0
        111.19
        24.72
        89.1%
        NA19461.assemble_contigs
        9.8Kbp
        5.1Kbp
        81.5K
        178733.0K
        114.8Kbp
        2751.1Mbp
        1891.0
        110.49
        24.73
        89.1%
        NA19463.assemble_contigs
        8.2Kbp
        4.2Kbp
        95.9K
        210657.0K
        158.2Kbp
        2708.0Mbp
        1628.0
        108.24
        21.00
        87.9%
        NA19467.assemble_contigs
        9.7Kbp
        5.0Kbp
        81.3K
        178658.0K
        134.5Kbp
        2736.1Mbp
        1958.0
        110.66
        24.60
        88.6%
        NA19471.assemble_contigs
        9.5Kbp
        4.9Kbp
        84.1K
        183944.0K
        120.4Kbp
        2737.2Mbp
        1952.0
        111.47
        24.82
        88.6%
        NA19473.assemble_contigs
        9.2Kbp
        4.8Kbp
        86.0K
        188147.0K
        121.2Kbp
        2737.4Mbp
        1836.0
        110.59
        24.72
        88.6%
        SAMEA2580844.assemble_contigs
        6.1Kbp
        3.2Kbp
        130.0K
        283516.0K
        79.3Kbp
        2716.4Mbp
        1575.0
        111.19
        20.63
        87.9%
        SAMEA2580845.assemble_contigs
        5.6Kbp
        2.9Kbp
        141.3K
        308562.0K
        72.4Kbp
        2709.8Mbp
        1613.0
        110.68
        19.81
        87.7%
        SAMEA2580848.assemble_contigs
        5.8Kbp
        3.0Kbp
        136.1K
        297496.0K
        83.7Kbp
        2712.7Mbp
        1670.0
        109.22
        19.60
        87.8%
        SAMEA2580849.assemble_contigs
        9.5Kbp
        4.8Kbp
        82.6K
        183386.0K
        118.6Kbp
        2730.6Mbp
        1491.0
        110.00
        24.33
        88.4%
        SAMEA2580852.assemble_contigs
        5.8Kbp
        3.0Kbp
        135.9K
        296651.0K
        81.3Kbp
        2712.1Mbp
        1581.0
        108.18
        19.49
        87.8%
        SAMEA2580853.assemble_contigs
        5.7Kbp
        3.0Kbp
        138.4K
        302010.0K
        76.7Kbp
        2712.8Mbp
        1632.0
        108.50
        19.47
        87.8%
        SAMEA2580854.assemble_contigs
        5.9Kbp
        3.1Kbp
        134.3K
        293539.0K
        82.7Kbp
        2713.3Mbp
        1702.0
        108.29
        19.58
        87.9%
        SAMEA2580855.assemble_contigs
        6.0Kbp
        3.1Kbp
        132.4K
        288842.0K
        74.6Kbp
        2715.6Mbp
        1694.0
        107.96
        19.53
        87.9%
        SAMEA2580856.assemble_contigs
        5.7Kbp
        3.0Kbp
        137.9K
        302013.0K
        74.1Kbp
        2716.2Mbp
        1613.0
        107.93
        19.73
        87.9%
        SAMEA2580858.assemble_contigs
        2.0Kbp
        1.1Kbp
        372.8K
        791736.0K
        35.8Kbp
        2522.0Mbp
        1391.0
        103.45
        15.93
        80.4%
        SAMEA2580859.assemble_contigs
        3.9Kbp
        2.0Kbp
        200.2K
        439279.0K
        73.7Kbp
        2691.3Mbp
        1697.0
        105.49
        18.13
        86.6%
        SAMEA2580861.assemble_contigs
        2.1Kbp
        1.2Kbp
        353.1K
        752569.0K
        29.3Kbp
        2548.3Mbp
        1435.0
        104.40
        15.76
        81.4%
        SAMEA2580862.assemble_contigs
        2.0Kbp
        1.1Kbp
        375.1K
        795956.0K
        36.7Kbp
        2506.8Mbp
        1423.0
        104.43
        15.59
        80.0%
        + +
        + +
        +
        + + + + +
        + +

        + Number of Contigs + +

        + +

        This plot shows the number of contigs found for each assembly, broken + down by length.

        + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        +
        + + + +
        +

        BUSCO

        +

        BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

        + + + + +
        + +

        + Lineage: eukaryota_odb10 + +

        + + + + +
        + + +
        +
        loading..
        +
        + + +
        + + +
        + + + + +
        + +
        +
        + + +

        + + + + + MultiQC v1.9 + + - Written by Phil Ewels, + available on GitHub. +

        +

        + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

        +
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        + + + + + + + + + + + + + + diff --git a/dataAnalysis/multiQC/startingDataset/CARFmultiqc_report.html b/dataAnalysis/multiQC/startingDataset/CARFmultiqc_report.html new file mode 100644 index 0000000..446826a --- /dev/null +++ b/dataAnalysis/multiQC/startingDataset/CARFmultiqc_report.html @@ -0,0 +1,5830 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              + Bioinformatics (2016)
              + doi: 10.1093/bioinformatics/btw354
              + PMID: 27312411 +
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              This report was generated using MultiQC, version 1.11

              +

              You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

              +

              For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

              +

              You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

              +

              MultiQC is published in Bioinformatics:

              +
              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
              + Bioinformatics (2016)
              + doi: 10.1093/bioinformatics/btw354
              + PMID: 27312411 +
              +
              + +
              + +
              + + +
              + + + +

              + + + + +

              + + + +

              + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

              + + + + + + + + + + + +
              +

              Report + + generated on 2021-07-08, 10:42 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/intermediate/4d/0c63f3334396ed94ac2240f2cd1ca9

              + + +
              + + + + + + + +
              + + + + + + + + +
              +

              General Statistics

              + + + + + + + + + + + Showing 26/26 rows and 2/2 columns. + +
              +
              + +
              Sample NameN50 (Kbp)Length (Mbp)
              LP6005441_DNA_A08.assemble_contigs
              1.0Kbp
              1775.3Mbp
              LP6005441_DNA_B08.assemble_contigs
              0.9Kbp
              1767.6Mbp
              LP6005441_DNA_G02.assemble_contigs
              1.1Kbp
              2060.9Mbp
              LP6005441_DNA_H02.assemble_contigs
              1.1Kbp
              2057.6Mbp
              LP6005592_DNA_C03.assemble_contigs
              1.1Kbp
              1963.4Mbp
              SAMEA2580802.assemble_contigs
              3.9Kbp
              2697.1Mbp
              SAMEA2580803.assemble_contigs
              5.9Kbp
              2713.1Mbp
              SAMEA2580807.assemble_contigs
              5.9Kbp
              2712.8Mbp
              SAMEA2580808.assemble_contigs
              2.3Kbp
              2603.7Mbp
              SAMEA2580809.assemble_contigs
              9.2Kbp
              2737.4Mbp
              SAMEA2580813.assemble_contigs
              5.7Kbp
              2713.8Mbp
              SAMEA2580814.assemble_contigs
              5.3Kbp
              2684.3Mbp
              SAMEA2580815.assemble_contigs
              4.3Kbp
              2703.7Mbp
              SAMEA2580816.assemble_contigs
              5.1Kbp
              2688.7Mbp
              SAMEA2580818.assemble_contigs
              5.6Kbp
              2684.2Mbp
              SAMEA2580819.assemble_contigs
              5.5Kbp
              2688.3Mbp
              SAMEA2580820.assemble_contigs
              5.4Kbp
              2688.1Mbp
              SAMEA2580821.assemble_contigs
              3.5Kbp
              2692.6Mbp
              SAMEA2580822.assemble_contigs
              5.8Kbp
              2704.2Mbp
              SAMEA2580823.assemble_contigs
              5.0Kbp
              2703.5Mbp
              SAMEA2580830.assemble_contigs
              5.8Kbp
              2704.0Mbp
              SAMEA2580831.assemble_contigs
              6.0Kbp
              2699.3Mbp
              SAMEA2580834.assemble_contigs
              5.8Kbp
              2703.3Mbp
              SAMEA2580836.assemble_contigs
              5.8Kbp
              2703.9Mbp
              SAMEA3506072.assemble_contigs
              9.2Kbp
              2737.7Mbp
              SAMEA3506073.assemble_contigs
              10.2Kbp
              2738.9Mbp
              + + +
              + + + + + + +
              +

              QUAST

              +

              QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

              + + + + +
              + +

              + Assembly Statistics + +

              + + + + +
              + + + + + + + + + Showing 26/26 rows and 10/10 columns. + +
              +
              + +
              Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
              LP6005441_DNA_A08.assemble_contigs
              1.0Kbp
              0.7Kbp
              615.0K
              1163.5K
              17.2Kbp
              1775.3Mbp
              841.0
              87.50
              13.84
              56.8%
              LP6005441_DNA_B08.assemble_contigs
              0.9Kbp
              0.7Kbp
              655.9K
              1221.5K
              12.8Kbp
              1767.6Mbp
              762.0
              85.27
              13.48
              56.5%
              LP6005441_DNA_G02.assemble_contigs
              1.1Kbp
              0.8Kbp
              573.5K
              1127.4K
              13.0Kbp
              2060.9Mbp
              1144.0
              88.07
              14.19
              65.8%
              LP6005441_DNA_H02.assemble_contigs
              1.1Kbp
              0.8Kbp
              577.3K
              1133.2K
              17.3Kbp
              2057.6Mbp
              1198.0
              88.37
              14.18
              65.7%
              LP6005592_DNA_C03.assemble_contigs
              1.1Kbp
              0.7Kbp
              594.5K
              1150.1K
              12.9Kbp
              1963.4Mbp
              1052.0
              90.42
              14.00
              62.7%
              SAMEA2580802.assemble_contigs
              3.9Kbp
              2.1Kbp
              196.9K
              432.3K
              55.3Kbp
              2697.1Mbp
              1728.0
              113.06
              19.97
              86.7%
              SAMEA2580803.assemble_contigs
              5.9Kbp
              3.1Kbp
              134.9K
              294.0K
              63.9Kbp
              2713.1Mbp
              1728.0
              114.73
              20.86
              87.8%
              SAMEA2580807.assemble_contigs
              5.9Kbp
              3.1Kbp
              133.6K
              291.5K
              66.8Kbp
              2712.8Mbp
              1877.0
              114.54
              20.80
              87.8%
              SAMEA2580808.assemble_contigs
              2.3Kbp
              1.3Kbp
              330.3K
              708.9K
              46.3Kbp
              2603.7Mbp
              1594.0
              110.86
              18.01
              83.0%
              SAMEA2580809.assemble_contigs
              9.2Kbp
              4.7Kbp
              86.2K
              189.8K
              124.1Kbp
              2737.4Mbp
              1414.0
              113.70
              25.59
              88.6%
              SAMEA2580813.assemble_contigs
              5.7Kbp
              3.0Kbp
              139.3K
              303.6K
              60.5Kbp
              2713.8Mbp
              1793.0
              114.39
              20.69
              87.8%
              SAMEA2580814.assemble_contigs
              5.3Kbp
              2.8Kbp
              147.1K
              322.1K
              60.2Kbp
              2684.3Mbp
              1685.0
              110.83
              17.10
              87.0%
              SAMEA2580815.assemble_contigs
              4.3Kbp
              2.3Kbp
              182.9K
              399.0K
              53.6Kbp
              2703.7Mbp
              1770.0
              113.14
              20.02
              87.1%
              SAMEA2580816.assemble_contigs
              5.1Kbp
              2.7Kbp
              152.8K
              333.2K
              62.1Kbp
              2688.7Mbp
              1699.0
              112.17
              18.37
              87.0%
              SAMEA2580818.assemble_contigs
              5.6Kbp
              2.9Kbp
              140.3K
              306.5K
              79.1Kbp
              2684.2Mbp
              1547.0
              111.63
              18.19
              87.0%
              SAMEA2580819.assemble_contigs
              5.5Kbp
              2.9Kbp
              140.9K
              308.1K
              69.7Kbp
              2688.3Mbp
              1656.0
              113.09
              18.59
              87.1%
              SAMEA2580820.assemble_contigs
              5.4Kbp
              2.8Kbp
              143.9K
              314.4K
              64.1Kbp
              2688.1Mbp
              1567.0
              112.72
              18.42
              87.1%
              SAMEA2580821.assemble_contigs
              3.5Kbp
              1.9Kbp
              218.6K
              478.2K
              65.1Kbp
              2692.6Mbp
              1615.0
              112.56
              19.92
              86.4%
              SAMEA2580822.assemble_contigs
              5.8Kbp
              3.0Kbp
              136.6K
              298.3K
              73.7Kbp
              2704.2Mbp
              1685.0
              113.64
              19.52
              87.6%
              SAMEA2580823.assemble_contigs
              5.0Kbp
              2.6Kbp
              159.0K
              346.5K
              60.7Kbp
              2703.5Mbp
              1731.0
              113.67
              20.10
              87.3%
              SAMEA2580830.assemble_contigs
              5.8Kbp
              3.0Kbp
              135.8K
              296.6K
              68.4Kbp
              2704.0Mbp
              1681.0
              115.61
              19.82
              87.6%
              SAMEA2580831.assemble_contigs
              6.0Kbp
              3.1Kbp
              130.5K
              284.7K
              69.9Kbp
              2699.3Mbp
              1641.0
              116.42
              21.34
              87.4%
              SAMEA2580834.assemble_contigs
              5.8Kbp
              3.0Kbp
              135.5K
              296.0K
              61.8Kbp
              2703.3Mbp
              1675.0
              115.94
              19.81
              87.6%
              SAMEA2580836.assemble_contigs
              5.8Kbp
              3.0Kbp
              135.6K
              296.2K
              66.3Kbp
              2703.9Mbp
              1723.0
              115.54
              19.78
              87.6%
              SAMEA3506072.assemble_contigs
              9.2Kbp
              4.7Kbp
              85.7K
              188.9K
              109.5Kbp
              2737.7Mbp
              1518.0
              114.24
              25.36
              88.7%
              SAMEA3506073.assemble_contigs
              10.2Kbp
              5.2Kbp
              78.0K
              172.0K
              126.3Kbp
              2738.9Mbp
              1607.0
              115.45
              25.72
              88.8%
              + +
              + +
              +
              + + + + +
              + +

              + Number of Contigs + +

              + +

              This plot shows the number of contigs found for each assembly, broken + down by length.

              + + +
              + + +
              +
              loading..
              +
              + + +
              + + +
              + + + + +
              + +
              +
              + + +

              + + + + + MultiQC v1.11 + + - Written by Phil Ewels, + available on GitHub. +

              +

              + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

              +
              +
              + + + + + + + + + + + + + + diff --git a/dataAnalysis/multiQC/startingDataset/CWNCmultiqc_report.html b/dataAnalysis/multiQC/startingDataset/CWNCmultiqc_report.html new file mode 100644 index 0000000..261fbae --- /dev/null +++ b/dataAnalysis/multiQC/startingDataset/CWNCmultiqc_report.html @@ -0,0 +1,5290 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                    If you use plots from MultiQC in a publication or presentation, please cite:

                    +
                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                    + Bioinformatics (2016)
                    + doi: 10.1093/bioinformatics/btw354
                    + PMID: 27312411 +
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                    About MultiQC

                    +

                    This report was generated using MultiQC, version 1.9

                    +

                    You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                    +

                    For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                    +

                    You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                    +

                    MultiQC is published in Bioinformatics:

                    +
                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                    + Bioinformatics (2016)
                    + doi: 10.1093/bioinformatics/btw354
                    + PMID: 27312411 +
                    +
                    + +
                    + +
                    + + +
                    + + + +

                    + + + + +

                    + + + +

                    + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                    + + + + + + + + + + + +
                    +

                    Report + + generated on 2022-03-30, 10:49 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/CWNC

                    + + +
                    + + + + + + + +
                    + + + + + + + + +
                    +

                    General Statistics

                    + + + + + + + + + + Showing 54/54 rows and 2/2 columns. + +
                    +
                    + +
                    Sample NameN50 (Kbp)Length (Mbp)
                    10_150304_L001.assemble_contigs
                    1.2Kbp
                    1904.1Mbp
                    11_150302_L002.assemble_contigs
                    1.0Kbp
                    1584.3Mbp
                    12_150304_L004.assemble_contigs
                    1.2Kbp
                    1945.6Mbp
                    13_RB103T_C_150611_L007.assemble_contigs
                    1.3Kbp
                    2097.9Mbp
                    14_150304_L001.assemble_contigs
                    1.0Kbp
                    1839.8Mbp
                    16_RB106T_C_150611_L008.assemble_contigs
                    1.0Kbp
                    1709.8Mbp
                    17_150304_L002.assemble_contigs
                    1.1Kbp
                    1812.4Mbp
                    18_RB108T_C_150611_L008.assemble_contigs
                    1.1Kbp
                    1872.0Mbp
                    20_150302_L001.assemble_contigs
                    0.9Kbp
                    1519.5Mbp
                    22_150304_L004.assemble_contigs
                    1.2Kbp
                    1984.1Mbp
                    24_RB114T_C_150616_L001.assemble_contigs
                    0.6Kbp
                    265.1Mbp
                    24_RB114T_C_150616_L002.assemble_contigs
                    0.6Kbp
                    300.6Mbp
                    25_RB115T_C_150616_L001.assemble_contigs
                    0.6Kbp
                    239.3Mbp
                    25_RB115T_C_150616_L002.assemble_contigs
                    0.6Kbp
                    270.3Mbp
                    26_RB116T_C_150616_L001.assemble_contigs
                    0.9Kbp
                    1326.3Mbp
                    26_RB116T_C_150616_L002.assemble_contigs
                    0.9Kbp
                    1395.1Mbp
                    27_150304_L003.assemble_contigs
                    1.1Kbp
                    1879.0Mbp
                    28_RB118T_C_150616_L003.assemble_contigs
                    1.4Kbp
                    2010.9Mbp
                    29_RB119T_C_150616_L003.assemble_contigs
                    0.9Kbp
                    1320.9Mbp
                    30_RB122T_C_150616_L004.assemble_contigs
                    1.4Kbp
                    2049.0Mbp
                    31_150304_L003.assemble_contigs
                    1.0Kbp
                    1720.9Mbp
                    32_RB124T_C_150616_L004.assemble_contigs
                    0.8Kbp
                    630.2Mbp
                    37_RB142T_C_150616_L005.assemble_contigs
                    1.0Kbp
                    1510.5Mbp
                    38_RB151T_C_150616_L005.assemble_contigs
                    1.2Kbp
                    1821.4Mbp
                    39_150304_L002.assemble_contigs
                    1.3Kbp
                    1916.0Mbp
                    4_RB091T_C_150611_L006.assemble_contigs
                    1.0Kbp
                    1747.5Mbp
                    5_150302_L001.assemble_contigs
                    1.0Kbp
                    1718.1Mbp
                    6_150302_L002.assemble_contigs
                    1.0Kbp
                    1549.2Mbp
                    7_RB094T_C_150611_L006.assemble_contigs
                    1.0Kbp
                    1715.7Mbp
                    CB12.assemble_contigs
                    6.7Kbp
                    2693.0Mbp
                    CB14.assemble_contigs
                    6.4Kbp
                    2674.9Mbp
                    CB15.assemble_contigs
                    6.5Kbp
                    2692.6Mbp
                    CB16.assemble_contigs
                    6.3Kbp
                    2689.1Mbp
                    CB17.assemble_contigs
                    4.9Kbp
                    2699.5Mbp
                    CB24.assemble_contigs
                    6.6Kbp
                    2692.1Mbp
                    CB29.assemble_contigs
                    5.3Kbp
                    2698.7Mbp
                    CB31.assemble_contigs
                    6.5Kbp
                    2690.9Mbp
                    CB32.assemble_contigs
                    5.4Kbp
                    2682.4Mbp
                    CB33.assemble_contigs
                    6.5Kbp
                    2676.9Mbp
                    CB7.assemble_contigs
                    6.3Kbp
                    2677.7Mbp
                    CF24.assemble_contigs
                    6.4Kbp
                    2689.1Mbp
                    CF25.assemble_contigs
                    6.4Kbp
                    2689.5Mbp
                    CF26.assemble_contigs
                    6.2Kbp
                    2680.6Mbp
                    CF27.assemble_contigs
                    6.3Kbp
                    2692.9Mbp
                    CF30.assemble_contigs
                    6.7Kbp
                    2691.1Mbp
                    CF37.assemble_contigs
                    6.5Kbp
                    2688.5Mbp
                    CF46.assemble_contigs
                    6.2Kbp
                    2671.4Mbp
                    CF49.assemble_contigs
                    6.3Kbp
                    2673.5Mbp
                    CP17.assemble_contigs
                    6.0Kbp
                    2672.2Mbp
                    CP28.assemble_contigs
                    6.7Kbp
                    2691.5Mbp
                    CP36.assemble_contigs
                    5.8Kbp
                    2679.1Mbp
                    CP38.assemble_contigs
                    5.9Kbp
                    2679.4Mbp
                    CP40.assemble_contigs
                    5.4Kbp
                    2698.9Mbp
                    CP48.assemble_contigs
                    5.9Kbp
                    2679.7Mbp
                    + + +
                    + + + + + + +
                    +

                    QUAST

                    +

                    QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                    + + + + +
                    + +

                    + Assembly Statistics + +

                    + + + + +
                    + + + + + + + + + Showing 54/54 rows and 10/10 columns. + +
                    +
                    + +
                    Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                    10_150304_L001.assemble_contigs
                    1.2Kbp
                    0.8Kbp
                    509.6K
                    1006234.0K
                    24.2Kbp
                    1904.1Mbp
                    1511.0
                    99.85
                    14.72
                    61.4%
                    11_150302_L002.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    524.3K
                    998095.0K
                    11.7Kbp
                    1584.3Mbp
                    1228.0
                    93.49
                    12.66
                    51.3%
                    12_150304_L004.assemble_contigs
                    1.2Kbp
                    0.8Kbp
                    517.9K
                    1023760.0K
                    14.5Kbp
                    1945.6Mbp
                    1439.0
                    96.38
                    14.00
                    62.7%
                    13_RB103T_C_150611_L007.assemble_contigs
                    1.3Kbp
                    0.8Kbp
                    485.4K
                    982253.0K
                    19.0Kbp
                    2097.9Mbp
                    1652.0
                    99.54
                    14.24
                    67.4%
                    14_150304_L001.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    587.9K
                    1116876.0K
                    18.1Kbp
                    1839.8Mbp
                    1559.0
                    95.43
                    13.70
                    59.4%
                    16_RB106T_C_150611_L008.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    540.4K
                    1032609.0K
                    12.0Kbp
                    1709.8Mbp
                    1406.0
                    96.26
                    13.08
                    55.3%
                    17_150304_L002.assemble_contigs
                    1.1Kbp
                    0.7Kbp
                    546.7K
                    1054633.0K
                    17.1Kbp
                    1812.4Mbp
                    1402.0
                    94.77
                    13.78
                    58.5%
                    18_RB108T_C_150611_L008.assemble_contigs
                    1.1Kbp
                    0.8Kbp
                    535.4K
                    1045600.0K
                    12.8Kbp
                    1872.0Mbp
                    1518.0
                    95.63
                    13.90
                    60.4%
                    20_150302_L001.assemble_contigs
                    0.9Kbp
                    0.7Kbp
                    558.0K
                    1037670.0K
                    11.2Kbp
                    1519.5Mbp
                    1230.0
                    92.93
                    12.68
                    49.3%
                    22_150304_L004.assemble_contigs
                    1.2Kbp
                    0.8Kbp
                    500.2K
                    997127.0K
                    15.7Kbp
                    1984.1Mbp
                    1465.0
                    98.21
                    14.35
                    63.9%
                    24_RB114T_C_150616_L001.assemble_contigs
                    0.6Kbp
                    0.6Kbp
                    164.6K
                    276029.0K
                    8.6Kbp
                    265.1Mbp
                    404.0
                    97.28
                    9.98
                    8.7%
                    24_RB114T_C_150616_L002.assemble_contigs
                    0.6Kbp
                    0.6Kbp
                    183.7K
                    308956.0K
                    9.2Kbp
                    300.6Mbp
                    470.0
                    96.14
                    10.12
                    9.8%
                    25_RB115T_C_150616_L001.assemble_contigs
                    0.6Kbp
                    0.6Kbp
                    149.3K
                    250120.0K
                    8.9Kbp
                    239.3Mbp
                    375.0
                    93.32
                    10.08
                    7.8%
                    25_RB115T_C_150616_L002.assemble_contigs
                    0.6Kbp
                    0.6Kbp
                    165.9K
                    278903.0K
                    6.5Kbp
                    270.3Mbp
                    378.0
                    92.22
                    9.99
                    8.8%
                    26_RB116T_C_150616_L001.assemble_contigs
                    0.9Kbp
                    0.7Kbp
                    518.1K
                    957300.0K
                    10.3Kbp
                    1326.3Mbp
                    1205.0
                    93.48
                    12.60
                    43.1%
                    26_RB116T_C_150616_L002.assemble_contigs
                    0.9Kbp
                    0.7Kbp
                    525.6K
                    978108.0K
                    11.4Kbp
                    1395.1Mbp
                    1292.0
                    93.94
                    12.63
                    45.3%
                    27_150304_L003.assemble_contigs
                    1.1Kbp
                    0.8Kbp
                    560.6K
                    1081855.0K
                    14.5Kbp
                    1879.0Mbp
                    1506.0
                    95.02
                    13.83
                    60.7%
                    28_RB118T_C_150616_L003.assemble_contigs
                    1.4Kbp
                    0.9Kbp
                    434.6K
                    895124.0K
                    22.1Kbp
                    2010.9Mbp
                    1559.0
                    97.41
                    14.07
                    64.6%
                    29_RB119T_C_150616_L003.assemble_contigs
                    0.9Kbp
                    0.7Kbp
                    501.0K
                    924986.0K
                    12.2Kbp
                    1320.9Mbp
                    1049.0
                    93.74
                    12.44
                    42.9%
                    30_RB122T_C_150616_L004.assemble_contigs
                    1.4Kbp
                    0.9Kbp
                    419.1K
                    876680.0K
                    23.3Kbp
                    2049.0Mbp
                    1490.0
                    99.56
                    14.46
                    65.8%
                    31_150304_L003.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    547.5K
                    1043436.0K
                    12.4Kbp
                    1720.9Mbp
                    1326.0
                    96.01
                    13.61
                    55.6%
                    32_RB124T_C_150616_L004.assemble_contigs
                    0.8Kbp
                    0.6Kbp
                    307.3K
                    541613.0K
                    7.1Kbp
                    630.2Mbp
                    647.0
                    91.57
                    11.61
                    20.5%
                    37_RB142T_C_150616_L005.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    472.4K
                    909069.0K
                    11.9Kbp
                    1510.5Mbp
                    1218.0
                    92.53
                    12.57
                    48.8%
                    38_RB151T_C_150616_L005.assemble_contigs
                    1.2Kbp
                    0.8Kbp
                    485.5K
                    965089.0K
                    15.8Kbp
                    1821.4Mbp
                    1423.0
                    96.79
                    12.91
                    58.8%
                    39_150304_L002.assemble_contigs
                    1.3Kbp
                    0.8Kbp
                    468.8K
                    948459.0K
                    21.3Kbp
                    1916.0Mbp
                    1350.0
                    95.97
                    14.24
                    61.7%
                    4_RB091T_C_150611_L006.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    582.8K
                    1101317.0K
                    14.8Kbp
                    1747.5Mbp
                    1509.0
                    94.64
                    13.21
                    56.5%
                    5_150302_L001.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    546.2K
                    1044576.0K
                    13.4Kbp
                    1718.1Mbp
                    1373.0
                    94.55
                    13.17
                    55.5%
                    6_150302_L002.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    488.2K
                    938525.0K
                    27.6Kbp
                    1549.2Mbp
                    1213.0
                    97.44
                    12.30
                    50.1%
                    7_RB094T_C_150611_L006.assemble_contigs
                    1.0Kbp
                    0.7Kbp
                    534.8K
                    1028528.0K
                    12.6Kbp
                    1715.7Mbp
                    1413.0
                    96.21
                    13.79
                    55.4%
                    CB12.assemble_contigs
                    6.7Kbp
                    3.5Kbp
                    117.4K
                    256974.0K
                    75.6Kbp
                    2693.0Mbp
                    591.0
                    104.75
                    20.62
                    87.4%
                    CB14.assemble_contigs
                    6.4Kbp
                    3.4Kbp
                    121.2K
                    264667.0K
                    64.8Kbp
                    2674.9Mbp
                    553.0
                    104.47
                    20.19
                    86.8%
                    CB15.assemble_contigs
                    6.5Kbp
                    3.4Kbp
                    120.4K
                    263809.0K
                    101.2Kbp
                    2692.6Mbp
                    628.0
                    105.01
                    20.66
                    87.3%
                    CB16.assemble_contigs
                    6.3Kbp
                    3.3Kbp
                    123.2K
                    270417.0K
                    72.7Kbp
                    2689.1Mbp
                    587.0
                    104.23
                    20.25
                    87.2%
                    CB17.assemble_contigs
                    4.9Kbp
                    2.6Kbp
                    162.5K
                    351948.0K
                    71.4Kbp
                    2699.5Mbp
                    725.0
                    105.12
                    20.73
                    87.0%
                    CB24.assemble_contigs
                    6.6Kbp
                    3.4Kbp
                    118.0K
                    258410.0K
                    74.9Kbp
                    2692.1Mbp
                    693.0
                    104.59
                    20.33
                    87.3%
                    CB29.assemble_contigs
                    5.3Kbp
                    2.8Kbp
                    148.4K
                    322099.0K
                    65.4Kbp
                    2698.7Mbp
                    648.0
                    104.36
                    20.31
                    87.1%
                    CB31.assemble_contigs
                    6.5Kbp
                    3.4Kbp
                    119.7K
                    262297.0K
                    77.5Kbp
                    2690.9Mbp
                    625.0
                    104.44
                    20.30
                    87.3%
                    CB32.assemble_contigs
                    5.4Kbp
                    2.9Kbp
                    145.1K
                    315052.0K
                    78.1Kbp
                    2682.4Mbp
                    686.0
                    104.88
                    20.46
                    86.7%
                    CB33.assemble_contigs
                    6.5Kbp
                    3.4Kbp
                    120.9K
                    264336.0K
                    68.5Kbp
                    2676.9Mbp
                    611.0
                    104.70
                    20.27
                    86.8%
                    CB7.assemble_contigs
                    6.3Kbp
                    3.3Kbp
                    123.0K
                    268438.0K
                    76.2Kbp
                    2677.7Mbp
                    607.0
                    104.89
                    20.30
                    86.8%
                    CF24.assemble_contigs
                    6.4Kbp
                    3.3Kbp
                    121.0K
                    265419.0K
                    78.7Kbp
                    2689.1Mbp
                    613.0
                    104.11
                    20.29
                    87.2%
                    CF25.assemble_contigs
                    6.4Kbp
                    3.3Kbp
                    121.6K
                    267194.0K
                    80.5Kbp
                    2689.5Mbp
                    594.0
                    103.85
                    20.40
                    87.2%
                    CF26.assemble_contigs
                    6.2Kbp
                    3.3Kbp
                    125.2K
                    273508.0K
                    68.5Kbp
                    2680.6Mbp
                    707.0
                    104.61
                    20.40
                    86.9%
                    CF27.assemble_contigs
                    6.3Kbp
                    3.3Kbp
                    124.8K
                    272860.0K
                    82.5Kbp
                    2692.9Mbp
                    679.0
                    104.41
                    20.39
                    87.3%
                    CF30.assemble_contigs
                    6.7Kbp
                    3.5Kbp
                    117.2K
                    256576.0K
                    70.5Kbp
                    2691.1Mbp
                    608.0
                    103.95
                    20.40
                    87.3%
                    CF37.assemble_contigs
                    6.5Kbp
                    3.4Kbp
                    119.5K
                    262693.0K
                    76.4Kbp
                    2688.5Mbp
                    590.0
                    103.79
                    20.26
                    87.2%
                    CF46.assemble_contigs
                    6.2Kbp
                    3.3Kbp
                    124.6K
                    272103.0K
                    75.1Kbp
                    2671.4Mbp
                    675.0
                    104.22
                    20.06
                    86.6%
                    CF49.assemble_contigs
                    6.3Kbp
                    3.3Kbp
                    124.5K
                    272252.0K
                    74.3Kbp
                    2673.5Mbp
                    599.0
                    103.89
                    20.06
                    86.7%
                    CP17.assemble_contigs
                    6.0Kbp
                    3.1Kbp
                    129.4K
                    283668.0K
                    67.2Kbp
                    2672.2Mbp
                    670.0
                    103.99
                    20.23
                    86.6%
                    CP28.assemble_contigs
                    6.7Kbp
                    3.5Kbp
                    116.8K
                    256117.0K
                    82.6Kbp
                    2691.5Mbp
                    601.0
                    104.29
                    20.40
                    87.3%
                    CP36.assemble_contigs
                    5.8Kbp
                    3.1Kbp
                    135.2K
                    293793.0K
                    60.7Kbp
                    2679.1Mbp
                    673.0
                    104.08
                    20.14
                    86.7%
                    CP38.assemble_contigs
                    5.9Kbp
                    3.1Kbp
                    132.0K
                    287627.0K
                    82.4Kbp
                    2679.4Mbp
                    627.0
                    104.19
                    20.17
                    86.8%
                    CP40.assemble_contigs
                    5.4Kbp
                    2.9Kbp
                    146.4K
                    317450.0K
                    61.1Kbp
                    2698.9Mbp
                    707.0
                    104.61
                    20.50
                    87.2%
                    CP48.assemble_contigs
                    5.9Kbp
                    3.1Kbp
                    133.2K
                    290184.0K
                    71.0Kbp
                    2679.7Mbp
                    616.0
                    104.68
                    20.37
                    86.7%
                    + +
                    + +
                    +
                    + + + + +
                    + +

                    + Number of Contigs + +

                    + +

                    This plot shows the number of contigs found for each assembly, broken + down by length.

                    + + +
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                    +
                    loading..
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                    + + +
                    + + +
                    +
                    + + + +
                    +

                    BUSCO

                    +

                    BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

                    + + + + +
                    + +

                    + Lineage: eukaryota_odb10 + +

                    + + + + +
                    + + +
                    +
                    loading..
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                    + + +
                    + + +
                    + + + + +
                    + +
                    +
                    + + +

                    + + + + + MultiQC v1.9 + + - Written by Phil Ewels, + available on GitHub. +

                    +

                    + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                          + Bioinformatics (2016)
                          + doi: 10.1093/bioinformatics/btw354
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                          +
                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                          + Bioinformatics (2016)
                          + doi: 10.1093/bioinformatics/btw354
                          + PMID: 27312411 +
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                          + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

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                          Report + + generated on 2022-03-30, 11:10 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/EAAA

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                          +

                          General Statistics

                          + + + + + + + + + + Showing 29/29 rows and 2/2 columns. + +
                          +
                          + +
                          Sample NameN50 (Kbp)Length (Mbp)
                          LP6005442_DNA_D09.assemble_contigs
                          1.1Kbp
                          2101.9Mbp
                          egpg5305762.assemble_contigs
                          1.7Kbp
                          2016.7Mbp
                          egpg5305763.assemble_contigs
                          0.7Kbp
                          451.1Mbp
                          egpg5305765.assemble_contigs
                          0.7Kbp
                          533.7Mbp
                          egpg5305770.assemble_contigs
                          0.6Kbp
                          214.3Mbp
                          egpg5305771.assemble_contigs
                          0.6Kbp
                          181.3Mbp
                          egpg5305773.assemble_contigs
                          0.6Kbp
                          140.1Mbp
                          egpg5305778.assemble_contigs
                          0.7Kbp
                          577.4Mbp
                          egpg5305781.assemble_contigs
                          0.7Kbp
                          405.2Mbp
                          egpg5305904.assemble_contigs
                          0.7Kbp
                          612.4Mbp
                          egpg5305910.assemble_contigs
                          0.7Kbp
                          459.5Mbp
                          egpg5305911.assemble_contigs
                          0.7Kbp
                          602.1Mbp
                          egpg5305918.assemble_contigs
                          0.7Kbp
                          478.6Mbp
                          egpg5305919.assemble_contigs
                          0.7Kbp
                          401.9Mbp
                          egpg5305920.assemble_contigs
                          1.3Kbp
                          2070.7Mbp
                          egpg5305936.assemble_contigs
                          0.7Kbp
                          451.7Mbp
                          egpg5305937.assemble_contigs
                          0.7Kbp
                          652.4Mbp
                          egpg5305944.assemble_contigs
                          0.8Kbp
                          634.0Mbp
                          egpg5305945.assemble_contigs
                          0.7Kbp
                          622.2Mbp
                          egpg5305949.assemble_contigs
                          1.3Kbp
                          2036.2Mbp
                          egpg5305952.assemble_contigs
                          0.8Kbp
                          792.3Mbp
                          egpg5305953.assemble_contigs
                          0.7Kbp
                          627.3Mbp
                          egpg5305959.assemble_contigs
                          0.7Kbp
                          364.6Mbp
                          egpg5305960.assemble_contigs
                          0.7Kbp
                          317.2Mbp
                          egpg5305961.assemble_contigs
                          0.7Kbp
                          521.3Mbp
                          egpg5305967.assemble_contigs
                          0.7Kbp
                          440.7Mbp
                          egpg5305968.assemble_contigs
                          0.7Kbp
                          362.6Mbp
                          egpg5305969.assemble_contigs
                          0.6Kbp
                          317.6Mbp
                          egpg5305974.assemble_contigs
                          1.5Kbp
                          2292.4Mbp
                          + + +
                          + + + + + + +
                          +

                          QUAST

                          +

                          QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                          + + + + +
                          + +

                          + Assembly Statistics + +

                          + + + + +
                          + + + + + + + + + Showing 29/29 rows and 10/10 columns. + +
                          +
                          + +
                          Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                          LP6005442_DNA_D09.assemble_contigs
                          1.1Kbp
                          0.8Kbp
                          597.4K
                          1169285.0K
                          12.6Kbp
                          2101.9Mbp
                          1063.0
                          77.87
                          12.51
                          67.1%
                          egpg5305762.assemble_contigs
                          1.7Kbp
                          1.0Kbp
                          359.1K
                          753908.0K
                          30.8Kbp
                          2016.7Mbp
                          1504.0
                          91.17
                          13.97
                          64.8%
                          egpg5305763.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          259.5K
                          442401.0K
                          9.5Kbp
                          451.1Mbp
                          334.0
                          77.17
                          8.50
                          14.7%
                          egpg5305765.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          292.0K
                          503146.0K
                          11.9Kbp
                          533.7Mbp
                          319.0
                          75.30
                          8.87
                          17.4%
                          egpg5305770.assemble_contigs
                          0.6Kbp
                          0.6Kbp
                          135.3K
                          226067.0K
                          6.4Kbp
                          214.3Mbp
                          229.0
                          78.48
                          8.44
                          7.0%
                          egpg5305771.assemble_contigs
                          0.6Kbp
                          0.6Kbp
                          118.3K
                          196280.0K
                          5.1Kbp
                          181.3Mbp
                          177.0
                          78.91
                          8.64
                          5.9%
                          egpg5305773.assemble_contigs
                          0.6Kbp
                          0.6Kbp
                          90.1K
                          149798.0K
                          4.5Kbp
                          140.1Mbp
                          126.0
                          74.60
                          9.30
                          4.6%
                          egpg5305778.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          317.5K
                          546442.0K
                          10.3Kbp
                          577.4Mbp
                          359.0
                          74.57
                          9.16
                          18.8%
                          egpg5305781.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          225.0K
                          386231.0K
                          4.6Kbp
                          405.2Mbp
                          227.0
                          75.14
                          9.53
                          13.2%
                          egpg5305904.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          330.5K
                          570137.0K
                          8.7Kbp
                          612.4Mbp
                          369.0
                          73.75
                          8.60
                          19.9%
                          egpg5305910.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          266.1K
                          452703.0K
                          6.3Kbp
                          459.5Mbp
                          332.0
                          74.23
                          8.40
                          15.0%
                          egpg5305911.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          329.6K
                          567203.0K
                          11.3Kbp
                          602.1Mbp
                          385.0
                          76.52
                          8.77
                          19.6%
                          egpg5305918.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          277.3K
                          471234.0K
                          5.4Kbp
                          478.6Mbp
                          275.0
                          74.67
                          8.66
                          15.6%
                          egpg5305919.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          241.9K
                          407736.0K
                          5.2Kbp
                          401.9Mbp
                          229.0
                          73.92
                          8.44
                          13.1%
                          egpg5305920.assemble_contigs
                          1.3Kbp
                          0.9Kbp
                          473.3K
                          962703.0K
                          24.5Kbp
                          2070.7Mbp
                          1454.0
                          86.94
                          12.59
                          66.7%
                          egpg5305936.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          255.6K
                          437117.0K
                          8.6Kbp
                          451.7Mbp
                          349.0
                          77.77
                          8.80
                          14.7%
                          egpg5305937.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          349.4K
                          603841.0K
                          4.8Kbp
                          652.4Mbp
                          342.0
                          74.32
                          8.98
                          21.2%
                          egpg5305944.assemble_contigs
                          0.8Kbp
                          0.6Kbp
                          305.4K
                          539778.0K
                          10.0Kbp
                          634.0Mbp
                          334.0
                          77.69
                          10.19
                          20.6%
                          egpg5305945.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          327.8K
                          568616.0K
                          6.2Kbp
                          622.2Mbp
                          299.0
                          76.16
                          9.62
                          20.3%
                          egpg5305949.assemble_contigs
                          1.3Kbp
                          0.8Kbp
                          482.7K
                          975338.0K
                          45.4Kbp
                          2036.2Mbp
                          1581.0
                          86.48
                          12.03
                          65.5%
                          egpg5305952.assemble_contigs
                          0.8Kbp
                          0.6Kbp
                          378.1K
                          669546.0K
                          4.8Kbp
                          792.3Mbp
                          380.0
                          76.85
                          9.69
                          25.7%
                          egpg5305953.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          345.6K
                          593350.0K
                          5.9Kbp
                          627.3Mbp
                          316.0
                          74.67
                          8.85
                          20.4%
                          egpg5305959.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          218.9K
                          369261.0K
                          5.9Kbp
                          364.6Mbp
                          251.0
                          76.77
                          8.35
                          11.9%
                          egpg5305960.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          190.5K
                          321243.0K
                          6.2Kbp
                          317.2Mbp
                          232.0
                          75.86
                          8.33
                          10.3%
                          egpg5305961.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          296.0K
                          505352.0K
                          7.3Kbp
                          521.3Mbp
                          311.0
                          75.21
                          8.69
                          17.0%
                          egpg5305967.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          257.4K
                          436837.0K
                          7.2Kbp
                          440.7Mbp
                          294.0
                          75.46
                          8.47
                          14.4%
                          egpg5305968.assemble_contigs
                          0.7Kbp
                          0.6Kbp
                          218.9K
                          368770.0K
                          7.6Kbp
                          362.6Mbp
                          212.0
                          73.78
                          8.63
                          11.8%
                          egpg5305969.assemble_contigs
                          0.6Kbp
                          0.6Kbp
                          197.6K
                          330653.0K
                          6.8Kbp
                          317.6Mbp
                          226.0
                          73.47
                          8.17
                          10.4%
                          egpg5305974.assemble_contigs
                          1.5Kbp
                          0.9Kbp
                          446.3K
                          927781.0K
                          30.1Kbp
                          2292.4Mbp
                          1672.0
                          87.41
                          13.45
                          73.6%
                          + +
                          + +
                          +
                          + + + + +
                          + +

                          + Number of Contigs + +

                          + +

                          This plot shows the number of contigs found for each assembly, broken + down by length.

                          + + +
                          + + +
                          +
                          loading..
                          +
                          + + +
                          + + +
                          +
                          + + + +
                          +

                          BUSCO

                          +

                          BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

                          + + + + +
                          + +

                          + Lineage: eukaryota_odb10 + +

                          + + + + +
                          + + +
                          +
                          loading..
                          +
                          + + +
                          + + +
                          + + + + +
                          + +
                          +
                          + + +

                          + + + + + MultiQC v1.9 + + - Written by Phil Ewels, + available on GitHub. +

                          +

                          + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                + Bioinformatics (2016)
                                + doi: 10.1093/bioinformatics/btw354
                                + PMID: 27312411 +
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                                MultiQC is published in Bioinformatics:

                                +
                                + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                + Bioinformatics (2016)
                                + doi: 10.1093/bioinformatics/btw354
                                + PMID: 27312411 +
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                                + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

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                                Report + + generated on 2022-03-30, 11:10 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/EANS

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                                +

                                General Statistics

                                + + + + + + + + + + Showing 64/64 rows and 2/2 columns. + +
                                +
                                + +
                                Sample NameN50 (Kbp)Length (Mbp)
                                10_UO_113T_150731_L003.assemble_contigs
                                1.1Kbp
                                1884.2Mbp
                                12_UO_125T_150731_L004.assemble_contigs
                                1.1Kbp
                                824.2Mbp
                                13_UO_134T_150731_L005.assemble_contigs
                                1.3Kbp
                                2074.9Mbp
                                14_UO_136T_150731_L005.assemble_contigs
                                1.1Kbp
                                869.8Mbp
                                15_UO_140T_150731_L006.assemble_contigs
                                1.0Kbp
                                1568.7Mbp
                                16_UO_142T_150731_L006.assemble_contigs
                                1.2Kbp
                                1935.3Mbp
                                17_UO_144T_150731_L007.assemble_contigs
                                1.3Kbp
                                1974.7Mbp
                                18_UO_148T_150731_L007.assemble_contigs
                                1.1Kbp
                                1510.0Mbp
                                19_UO_153T_150813_L001.assemble_contigs
                                1.0Kbp
                                1584.2Mbp
                                1_UO_005T_150730_L001.assemble_contigs
                                1.2Kbp
                                1925.3Mbp
                                20_UO_157T_150813_L001.assemble_contigs
                                0.8Kbp
                                504.5Mbp
                                21_UO_006C_150813_L002.assemble_contigs
                                1.0Kbp
                                1479.7Mbp
                                22_UO_045C_150813_L002.assemble_contigs
                                1.3Kbp
                                1943.6Mbp
                                23_UO_064C_150813_L003.assemble_contigs
                                1.0Kbp
                                1657.0Mbp
                                24_UO_065C_150813_L003.assemble_contigs
                                1.0Kbp
                                1617.2Mbp
                                25_UO_068C_150813_L004.assemble_contigs
                                1.1Kbp
                                1690.0Mbp
                                26_UO_070C_150813_L004.assemble_contigs
                                1.1Kbp
                                1646.9Mbp
                                27_UO_072C_150813_L001.assemble_contigs
                                1.3Kbp
                                1999.4Mbp
                                28_UO_073C_150813_L001.assemble_contigs
                                1.0Kbp
                                1621.7Mbp
                                29_UO_075C_150813_L002.assemble_contigs
                                1.1Kbp
                                1031.5Mbp
                                2_UO_044T_150730_L001.assemble_contigs
                                1.0Kbp
                                1579.6Mbp
                                30_UO_077C_150813_L002.assemble_contigs
                                1.1Kbp
                                1830.0Mbp
                                31_UO_079C_150813_L003.assemble_contigs
                                1.0Kbp
                                1507.7Mbp
                                32_UO_080C_150813_L003.assemble_contigs
                                1.3Kbp
                                123.2Mbp
                                33_UO_082C_150813_L004.assemble_contigs
                                1.1Kbp
                                1782.2Mbp
                                34_UO_088C_150813_L004.assemble_contigs
                                1.1Kbp
                                1740.8Mbp
                                35_UO_090C_150813_L005.assemble_contigs
                                1.2Kbp
                                1912.0Mbp
                                36_UO_091C_150813_L005.assemble_contigs
                                1.1Kbp
                                1726.7Mbp
                                37_UO_092C_150902_L001.assemble_contigs
                                1.1Kbp
                                1762.9Mbp
                                38_UO_093C_150902_L001.assemble_contigs
                                1.1Kbp
                                1779.9Mbp
                                39_UO_098C_150902_L002.assemble_contigs
                                1.7Kbp
                                2181.8Mbp
                                3_UO_046T_150730_L002.assemble_contigs
                                1.1Kbp
                                1684.3Mbp
                                40_UO_099C_150902_L002.assemble_contigs
                                0.7Kbp
                                363.7Mbp
                                41_UO_100C_150902_L003.assemble_contigs
                                1.1Kbp
                                969.3Mbp
                                42_UO_105C_150902_L003.assemble_contigs
                                1.3Kbp
                                2035.2Mbp
                                43_UO_106C_150902_L004.assemble_contigs
                                1.1Kbp
                                1878.4Mbp
                                44_UO_107C_150902_L004.assemble_contigs
                                1.1Kbp
                                1873.6Mbp
                                45_UO_109C_150902_L005.assemble_contigs
                                1.1Kbp
                                1090.4Mbp
                                46_UO_114C_150902_L005.assemble_contigs
                                1.1Kbp
                                770.6Mbp
                                47_UO_115C_150902_L006.assemble_contigs
                                1.2Kbp
                                1989.4Mbp
                                48_UO_127C_150902_L006.assemble_contigs
                                1.0Kbp
                                650.3Mbp
                                49_UO_137C_150902_L007.assemble_contigs
                                1.0Kbp
                                1653.3Mbp
                                4_UO_048T_150730_L002.assemble_contigs
                                1.1Kbp
                                1051.0Mbp
                                50_UO_185C_150902_L007.assemble_contigs
                                1.1Kbp
                                1817.0Mbp
                                5_UO_063T_150731_L001.assemble_contigs
                                1.1Kbp
                                1530.7Mbp
                                6_UO_069T_150731_L001.assemble_contigs
                                1.3Kbp
                                2055.9Mbp
                                7_UO_071T_150731_L002.assemble_contigs
                                1.2Kbp
                                1914.9Mbp
                                8_UO_074T_150731_L002.assemble_contigs
                                1.1Kbp
                                1864.2Mbp
                                9_UO_076T_150731_L003.assemble_contigs
                                1.1Kbp
                                1788.7Mbp
                                LP6005442_DNA_F09.assemble_contigs
                                0.9Kbp
                                1811.0Mbp
                                LP6005443_DNA_E06.assemble_contigs
                                1.0Kbp
                                1840.8Mbp
                                LP6005443_DNA_F06.assemble_contigs
                                1.3Kbp
                                2166.7Mbp
                                LP6005677_DNA_G01.assemble_contigs
                                1.0Kbp
                                1814.6Mbp
                                egpg5305767.assemble_contigs
                                0.6Kbp
                                199.8Mbp
                                egpg5305775.assemble_contigs
                                0.6Kbp
                                124.8Mbp
                                egpg5305776.assemble_contigs
                                0.6Kbp
                                186.1Mbp
                                egpg5305783.assemble_contigs
                                0.8Kbp
                                464.6Mbp
                                egpg5305791.assemble_contigs
                                0.7Kbp
                                319.5Mbp
                                egpg5305792.assemble_contigs
                                0.6Kbp
                                22.6Mbp
                                egpg5305793.assemble_contigs
                                0.7Kbp
                                432.2Mbp
                                egpg5305798.assemble_contigs
                                0.6Kbp
                                311.8Mbp
                                egpg5305799.assemble_contigs
                                0.7Kbp
                                452.5Mbp
                                egpg5305814.assemble_contigs
                                1.2Kbp
                                2039.1Mbp
                                egpg5305831.assemble_contigs
                                0.7Kbp
                                459.8Mbp
                                + + +
                                + + + + + + +
                                +

                                QUAST

                                +

                                QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                + + + + +
                                + +

                                + Assembly Statistics + +

                                + + + + +
                                + + + + + + + + + Showing 64/64 rows and 10/10 columns. + +
                                +
                                + +
                                Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                10_UO_113T_150731_L003.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                546.5K
                                1056668.0K
                                13.2Kbp
                                1884.2Mbp
                                1499.0
                                95.00
                                13.57
                                60.8%
                                12_UO_125T_150731_L004.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                217.0K
                                447691.0K
                                23.5Kbp
                                824.2Mbp
                                947.0
                                111.53
                                14.00
                                26.5%
                                13_UO_134T_150731_L005.assemble_contigs
                                1.3Kbp
                                0.9Kbp
                                478.2K
                                965176.0K
                                21.8Kbp
                                2074.9Mbp
                                1534.0
                                98.68
                                14.20
                                66.7%
                                14_UO_136T_150731_L005.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                232.3K
                                476484.0K
                                35.5Kbp
                                869.8Mbp
                                945.0
                                108.97
                                13.85
                                28.0%
                                15_UO_140T_150731_L006.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                511.1K
                                970558.0K
                                11.2Kbp
                                1568.7Mbp
                                1244.0
                                97.24
                                12.52
                                50.7%
                                16_UO_142T_150731_L006.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                538.8K
                                1048888.0K
                                13.5Kbp
                                1935.3Mbp
                                1531.0
                                95.57
                                13.68
                                62.4%
                                17_UO_144T_150731_L007.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                491.4K
                                979240.0K
                                15.4Kbp
                                1974.7Mbp
                                1463.0
                                98.24
                                14.19
                                63.6%
                                18_UO_148T_150731_L007.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                417.8K
                                825230.0K
                                16.4Kbp
                                1510.0Mbp
                                1295.0
                                101.32
                                13.39
                                48.7%
                                19_UO_153T_150813_L001.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                520.2K
                                986962.0K
                                12.5Kbp
                                1584.2Mbp
                                1271.0
                                94.22
                                13.05
                                51.2%
                                1_UO_005T_150730_L001.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                497.1K
                                984211.0K
                                12.8Kbp
                                1925.3Mbp
                                1691.0
                                97.60
                                14.00
                                62.0%
                                20_UO_157T_150813_L001.assemble_contigs
                                0.8Kbp
                                0.6Kbp
                                196.6K
                                373848.0K
                                15.7Kbp
                                504.5Mbp
                                1328.0
                                114.21
                                15.93
                                16.3%
                                21_UO_006C_150813_L002.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                519.7K
                                974007.0K
                                15.1Kbp
                                1479.7Mbp
                                1239.0
                                91.82
                                13.03
                                47.9%
                                22_UO_045C_150813_L002.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                478.2K
                                957252.0K
                                15.8Kbp
                                1943.6Mbp
                                1493.0
                                98.16
                                14.30
                                62.5%
                                23_UO_064C_150813_L003.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                547.7K
                                1033783.0K
                                9.8Kbp
                                1657.0Mbp
                                1265.0
                                93.05
                                13.22
                                53.6%
                                24_UO_065C_150813_L003.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                557.4K
                                1044179.0K
                                11.5Kbp
                                1617.2Mbp
                                1393.0
                                94.07
                                12.61
                                52.3%
                                25_UO_068C_150813_L004.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                526.9K
                                1006518.0K
                                14.6Kbp
                                1690.0Mbp
                                1368.0
                                95.64
                                13.42
                                54.6%
                                26_UO_070C_150813_L004.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                496.7K
                                958266.0K
                                13.1Kbp
                                1646.9Mbp
                                1329.0
                                95.51
                                13.60
                                53.2%
                                27_UO_072C_150813_L001.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                501.3K
                                994548.0K
                                23.5Kbp
                                1999.4Mbp
                                1492.0
                                98.14
                                14.28
                                64.4%
                                28_UO_073C_150813_L001.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                527.3K
                                1000296.0K
                                13.3Kbp
                                1621.7Mbp
                                1339.0
                                94.93
                                13.23
                                52.4%
                                29_UO_075C_150813_L002.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                293.6K
                                586086.0K
                                16.1Kbp
                                1031.5Mbp
                                1057.0
                                105.81
                                13.33
                                33.3%
                                2_UO_044T_150730_L001.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                497.7K
                                953704.0K
                                11.9Kbp
                                1579.6Mbp
                                1363.0
                                95.17
                                13.46
                                51.1%
                                30_UO_077C_150813_L002.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                520.0K
                                1012758.0K
                                13.6Kbp
                                1830.0Mbp
                                1356.0
                                94.87
                                13.47
                                59.0%
                                31_UO_079C_150813_L003.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                534.2K
                                996186.0K
                                12.0Kbp
                                1507.7Mbp
                                1230.0
                                92.39
                                12.27
                                48.8%
                                32_UO_080C_150813_L003.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                30.1K
                                60128.0K
                                16.7Kbp
                                123.2Mbp
                                47.0
                                86.10
                                12.80
                                4.0%
                                33_UO_082C_150813_L004.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                500.3K
                                979293.0K
                                11.6Kbp
                                1782.2Mbp
                                1365.0
                                96.54
                                13.70
                                57.5%
                                34_UO_088C_150813_L004.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                523.6K
                                1008279.0K
                                11.4Kbp
                                1740.8Mbp
                                1427.0
                                95.73
                                13.57
                                56.2%
                                35_UO_090C_150813_L005.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                510.7K
                                1002879.0K
                                13.6Kbp
                                1912.0Mbp
                                1594.0
                                97.62
                                13.92
                                61.6%
                                36_UO_091C_150813_L005.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                530.7K
                                1015400.0K
                                12.3Kbp
                                1726.7Mbp
                                1380.0
                                95.95
                                13.41
                                55.8%
                                37_UO_092C_150902_L001.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                536.3K
                                1027662.0K
                                15.0Kbp
                                1762.9Mbp
                                1459.0
                                96.73
                                13.52
                                56.9%
                                38_UO_093C_150902_L001.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                535.9K
                                1028739.0K
                                13.9Kbp
                                1779.9Mbp
                                1601.0
                                97.39
                                13.83
                                57.4%
                                39_UO_098C_150902_L002.assemble_contigs
                                1.7Kbp
                                1.0Kbp
                                376.8K
                                805016.0K
                                24.9Kbp
                                2181.8Mbp
                                1622.0
                                101.30
                                14.27
                                70.1%
                                3_UO_046T_150730_L002.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                524.4K
                                1002311.0K
                                11.6Kbp
                                1684.3Mbp
                                1348.0
                                97.28
                                13.07
                                54.4%
                                40_UO_099C_150902_L002.assemble_contigs
                                0.7Kbp
                                0.6Kbp
                                200.7K
                                344164.0K
                                5.8Kbp
                                363.7Mbp
                                429.0
                                89.43
                                11.23
                                11.9%
                                41_UO_100C_150902_L003.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                266.8K
                                540620.0K
                                19.0Kbp
                                969.3Mbp
                                940.0
                                107.91
                                14.30
                                31.3%
                                42_UO_105C_150902_L003.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                508.3K
                                1007910.0K
                                21.7Kbp
                                2035.2Mbp
                                1542.0
                                98.82
                                14.17
                                65.5%
                                43_UO_106C_150902_L004.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                533.7K
                                1035125.0K
                                13.2Kbp
                                1878.4Mbp
                                1433.0
                                97.64
                                13.87
                                60.6%
                                44_UO_107C_150902_L004.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                535.9K
                                1037954.0K
                                13.2Kbp
                                1873.6Mbp
                                1552.0
                                97.02
                                13.66
                                60.4%
                                45_UO_109C_150902_L005.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                296.2K
                                599519.0K
                                21.9Kbp
                                1090.4Mbp
                                1117.0
                                106.88
                                13.72
                                35.1%
                                46_UO_114C_150902_L005.assemble_contigs
                                1.1Kbp
                                0.7Kbp
                                197.4K
                                411196.0K
                                27.9Kbp
                                770.6Mbp
                                938.0
                                111.36
                                14.26
                                24.8%
                                47_UO_115C_150902_L006.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                532.8K
                                1041725.0K
                                14.4Kbp
                                1989.4Mbp
                                1536.0
                                96.12
                                13.63
                                64.1%
                                48_UO_127C_150902_L006.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                187.6K
                                384482.0K
                                30.5Kbp
                                650.3Mbp
                                1157.0
                                114.74
                                14.78
                                20.9%
                                49_UO_137C_150902_L007.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                574.9K
                                1074422.0K
                                12.2Kbp
                                1653.3Mbp
                                1342.0
                                93.12
                                13.02
                                53.5%
                                4_UO_048T_150730_L002.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                269.2K
                                555536.0K
                                27.5Kbp
                                1051.0Mbp
                                1002.0
                                107.75
                                14.45
                                33.9%
                                50_UO_185C_150902_L007.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                515.1K
                                1006278.0K
                                16.1Kbp
                                1817.0Mbp
                                1338.0
                                96.80
                                13.73
                                58.6%
                                5_UO_063T_150731_L001.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                434.6K
                                854502.0K
                                15.5Kbp
                                1530.7Mbp
                                1231.0
                                101.17
                                13.24
                                49.4%
                                6_UO_069T_150731_L001.assemble_contigs
                                1.3Kbp
                                0.9Kbp
                                468.4K
                                949454.0K
                                18.4Kbp
                                2055.9Mbp
                                1501.0
                                98.67
                                14.34
                                66.1%
                                7_UO_071T_150731_L002.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                516.7K
                                1012133.0K
                                13.6Kbp
                                1914.9Mbp
                                1413.0
                                97.86
                                13.75
                                61.7%
                                8_UO_074T_150731_L002.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                519.1K
                                1015134.0K
                                13.8Kbp
                                1864.2Mbp
                                1471.0
                                95.18
                                13.45
                                60.1%
                                9_UO_076T_150731_L003.assemble_contigs
                                1.1Kbp
                                0.8Kbp
                                529.6K
                                1023588.0K
                                11.8Kbp
                                1788.7Mbp
                                1386.0
                                94.74
                                13.35
                                57.8%
                                LP6005442_DNA_F09.assemble_contigs
                                0.9Kbp
                                0.7Kbp
                                654.6K
                                1226660.0K
                                10.2Kbp
                                1811.0Mbp
                                907.0
                                77.25
                                11.93
                                57.9%
                                LP6005443_DNA_E06.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                617.3K
                                1172269.0K
                                15.2Kbp
                                1840.8Mbp
                                846.0
                                76.18
                                11.95
                                58.8%
                                LP6005443_DNA_F06.assemble_contigs
                                1.3Kbp
                                0.8Kbp
                                512.7K
                                1044461.0K
                                18.4Kbp
                                2166.7Mbp
                                1208.0
                                82.48
                                13.39
                                69.2%
                                LP6005677_DNA_G01.assemble_contigs
                                1.0Kbp
                                0.7Kbp
                                639.4K
                                1199146.0K
                                10.1Kbp
                                1814.6Mbp
                                919.0
                                79.29
                                12.01
                                58.0%
                                egpg5305767.assemble_contigs
                                0.6Kbp
                                0.6Kbp
                                126.7K
                                211776.0K
                                11.2Kbp
                                199.8Mbp
                                250.0
                                87.36
                                9.42
                                6.5%
                                egpg5305775.assemble_contigs
                                0.6Kbp
                                0.6Kbp
                                76.0K
                                128143.0K
                                3.3Kbp
                                124.8Mbp
                                97.0
                                87.26
                                9.76
                                4.1%
                                egpg5305776.assemble_contigs
                                0.6Kbp
                                0.6Kbp
                                115.2K
                                193341.0K
                                3.9Kbp
                                186.1Mbp
                                152.0
                                84.62
                                8.99
                                6.1%
                                egpg5305783.assemble_contigs
                                0.8Kbp
                                0.6Kbp
                                221.6K
                                394385.0K
                                7.4Kbp
                                464.6Mbp
                                276.0
                                88.05
                                9.91
                                15.1%
                                egpg5305791.assemble_contigs
                                0.7Kbp
                                0.6Kbp
                                164.4K
                                287861.0K
                                5.3Kbp
                                319.5Mbp
                                195.0
                                87.95
                                10.09
                                10.4%
                                egpg5305792.assemble_contigs
                                0.6Kbp
                                0.5Kbp
                                15.8K
                                25901.0K
                                10.8Kbp
                                22.6Mbp
                                50.0
                                105.37
                                18.38
                                0.7%
                                egpg5305793.assemble_contigs
                                0.7Kbp
                                0.6Kbp
                                227.5K
                                395670.0K
                                5.1Kbp
                                432.2Mbp
                                286.0
                                84.68
                                9.37
                                14.1%
                                egpg5305798.assemble_contigs
                                0.6Kbp
                                0.6Kbp
                                193.5K
                                324193.0K
                                8.1Kbp
                                311.8Mbp
                                273.0
                                80.45
                                8.60
                                10.2%
                                egpg5305799.assemble_contigs
                                0.7Kbp
                                0.6Kbp
                                219.9K
                                389634.0K
                                5.6Kbp
                                452.5Mbp
                                263.0
                                87.04
                                9.97
                                14.7%
                                egpg5305814.assemble_contigs
                                1.2Kbp
                                0.8Kbp
                                509.6K
                                1020495.0K
                                43.5Kbp
                                2039.1Mbp
                                1556.0
                                91.98
                                12.77
                                65.6%
                                egpg5305831.assemble_contigs
                                0.7Kbp
                                0.6Kbp
                                246.9K
                                427225.0K
                                10.9Kbp
                                459.8Mbp
                                295.0
                                84.19
                                9.34
                                15.0%
                                + +
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                                + Number of Contigs + +

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                                      +
                                      + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                      + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                      + Bioinformatics (2016)
                                      + doi: 10.1093/bioinformatics/btw354
                                      + PMID: 27312411 +
                                      +
                                      +
                                      + + +
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                                      +

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                                      +

                                      You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                                      +

                                      For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                      +

                                      You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                      +

                                      MultiQC is published in Bioinformatics:

                                      +
                                      + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                      + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                      + Bioinformatics (2016)
                                      + doi: 10.1093/bioinformatics/btw354
                                      + PMID: 27312411 +
                                      +
                                      + +
                                      + +
                                      + + +
                                      + + + +

                                      + + + + +

                                      + + + +

                                      + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                      + + + + + + + + + + + +
                                      +

                                      Report + + generated on 2022-03-30, 11:11 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/FWNC

                                      + + +
                                      + + + + + + + +
                                      + + + + + + + + +
                                      +

                                      General Statistics

                                      + + + + + + + + + + Showing 35/35 rows and 2/2 columns. + +
                                      +
                                      + +
                                      Sample NameN50 (Kbp)Length (Mbp)
                                      HG03225.assemble_contigs
                                      8.3Kbp
                                      2722.4Mbp
                                      HG03380.assemble_contigs
                                      8.1Kbp
                                      2705.7Mbp
                                      HG03385.assemble_contigs
                                      9.7Kbp
                                      2749.9Mbp
                                      HG03388.assemble_contigs
                                      8.3Kbp
                                      2720.8Mbp
                                      HG03449.assemble_contigs
                                      8.1Kbp
                                      2705.0Mbp
                                      IAJ0K.assemble_contigs
                                      6.4Kbp
                                      2673.4Mbp
                                      IAM0N.assemble_contigs
                                      6.4Kbp
                                      2674.2Mbp
                                      IAP0Q.assemble_contigs
                                      6.5Kbp
                                      2694.4Mbp
                                      IBJ0M.assemble_contigs
                                      6.3Kbp
                                      2673.2Mbp
                                      IBQ0T.assemble_contigs
                                      6.4Kbp
                                      2675.8Mbp
                                      LP6005441_DNA_F07.assemble_contigs
                                      1.0Kbp
                                      1948.4Mbp
                                      LZP0B.assemble_contigs
                                      6.8Kbp
                                      2691.8Mbp
                                      NA18498.assemble_contigs
                                      7.8Kbp
                                      2725.2Mbp
                                      NA18499.assemble_contigs
                                      10.2Kbp
                                      2735.3Mbp
                                      NA18501.assemble_contigs
                                      7.5Kbp
                                      2726.0Mbp
                                      NA18504.assemble_contigs
                                      8.0Kbp
                                      2722.1Mbp
                                      NA18505.assemble_contigs
                                      8.1Kbp
                                      2701.5Mbp
                                      NA19099.assemble_contigs
                                      8.5Kbp
                                      2703.3Mbp
                                      NA19107.assemble_contigs
                                      9.3Kbp
                                      2750.0Mbp
                                      NA19118.assemble_contigs
                                      8.4Kbp
                                      2703.0Mbp
                                      NA19129.assemble_contigs
                                      10.8Kbp
                                      2734.4Mbp
                                      NA19131.assemble_contigs
                                      12.0Kbp
                                      2732.8Mbp
                                      PAV0Q.assemble_contigs
                                      6.7Kbp
                                      2693.0Mbp
                                      PAZ0V.assemble_contigs
                                      6.7Kbp
                                      2677.5Mbp
                                      PBA0X.assemble_contigs
                                      6.8Kbp
                                      2692.6Mbp
                                      PBC0A.assemble_contigs
                                      6.7Kbp
                                      2677.5Mbp
                                      SAMEA2580885.assemble_contigs
                                      4.9Kbp
                                      2720.3Mbp
                                      SAMEA2580886.assemble_contigs
                                      5.8Kbp
                                      2719.7Mbp
                                      SAMEA2580889.assemble_contigs
                                      5.8Kbp
                                      2714.4Mbp
                                      SAMEA2580891.assemble_contigs
                                      5.9Kbp
                                      2699.9Mbp
                                      SAMEA2580897.assemble_contigs
                                      7.9Kbp
                                      2726.5Mbp
                                      SAMEA3506075.assemble_contigs
                                      10.1Kbp
                                      2739.4Mbp
                                      SAMEA3506076.assemble_contigs
                                      10.8Kbp
                                      2722.1Mbp
                                      SAMEA3506077.assemble_contigs
                                      9.2Kbp
                                      2740.3Mbp
                                      SAMEA3506078.assemble_contigs
                                      7.6Kbp
                                      2741.2Mbp
                                      + + +
                                      + + + + + + +
                                      +

                                      QUAST

                                      +

                                      QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                      + + + + +
                                      + +

                                      + Assembly Statistics + +

                                      + + + + +
                                      + + + + + + + + + Showing 35/35 rows and 10/10 columns. + +
                                      +
                                      + +
                                      Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                      HG03225.assemble_contigs
                                      8.3Kbp
                                      4.3Kbp
                                      94.3K
                                      207705.0K
                                      120.4Kbp
                                      2722.4Mbp
                                      1692.0
                                      109.29
                                      21.41
                                      88.4%
                                      HG03380.assemble_contigs
                                      8.1Kbp
                                      4.2Kbp
                                      96.4K
                                      211765.0K
                                      137.0Kbp
                                      2705.7Mbp
                                      1587.0
                                      109.02
                                      21.21
                                      87.8%
                                      HG03385.assemble_contigs
                                      9.7Kbp
                                      5.0Kbp
                                      82.1K
                                      180547.0K
                                      175.1Kbp
                                      2749.9Mbp
                                      1838.0
                                      111.24
                                      24.88
                                      89.1%
                                      HG03388.assemble_contigs
                                      8.3Kbp
                                      4.3Kbp
                                      94.1K
                                      207498.0K
                                      196.0Kbp
                                      2720.8Mbp
                                      1697.0
                                      109.32
                                      21.38
                                      88.3%
                                      HG03449.assemble_contigs
                                      8.1Kbp
                                      4.2Kbp
                                      96.2K
                                      211409.0K
                                      129.9Kbp
                                      2705.0Mbp
                                      1573.0
                                      109.28
                                      21.15
                                      87.8%
                                      IAJ0K.assemble_contigs
                                      6.4Kbp
                                      3.3Kbp
                                      121.8K
                                      266515.0K
                                      69.7Kbp
                                      2673.4Mbp
                                      625.0
                                      103.44
                                      20.09
                                      86.7%
                                      IAM0N.assemble_contigs
                                      6.4Kbp
                                      3.3Kbp
                                      121.9K
                                      266615.0K
                                      82.8Kbp
                                      2674.2Mbp
                                      618.0
                                      103.26
                                      20.09
                                      86.7%
                                      IAP0Q.assemble_contigs
                                      6.5Kbp
                                      3.4Kbp
                                      119.9K
                                      263034.0K
                                      81.8Kbp
                                      2694.4Mbp
                                      684.0
                                      103.48
                                      20.44
                                      87.4%
                                      IBJ0M.assemble_contigs
                                      6.3Kbp
                                      3.3Kbp
                                      123.3K
                                      269460.0K
                                      73.1Kbp
                                      2673.2Mbp
                                      626.0
                                      103.39
                                      20.08
                                      86.7%
                                      IBQ0T.assemble_contigs
                                      6.4Kbp
                                      3.3Kbp
                                      121.5K
                                      266101.0K
                                      73.7Kbp
                                      2675.8Mbp
                                      586.0
                                      103.15
                                      20.18
                                      86.8%
                                      LP6005441_DNA_F07.assemble_contigs
                                      1.0Kbp
                                      0.7Kbp
                                      665.2K
                                      1255240.0K
                                      13.4Kbp
                                      1948.4Mbp
                                      1017.0
                                      78.10
                                      12.64
                                      62.2%
                                      LZP0B.assemble_contigs
                                      6.8Kbp
                                      3.5Kbp
                                      114.7K
                                      251744.0K
                                      77.6Kbp
                                      2691.8Mbp
                                      607.0
                                      103.48
                                      20.42
                                      87.4%
                                      NA18498.assemble_contigs
                                      7.8Kbp
                                      4.1Kbp
                                      100.6K
                                      220686.0K
                                      114.7Kbp
                                      2725.2Mbp
                                      1642.0
                                      108.34
                                      21.29
                                      88.4%
                                      NA18499.assemble_contigs
                                      10.2Kbp
                                      5.3Kbp
                                      77.9K
                                      170989.0K
                                      167.8Kbp
                                      2735.3Mbp
                                      1895.0
                                      111.11
                                      24.87
                                      88.6%
                                      NA18501.assemble_contigs
                                      7.5Kbp
                                      3.9Kbp
                                      105.1K
                                      231381.0K
                                      101.2Kbp
                                      2726.0Mbp
                                      1719.0
                                      108.86
                                      21.32
                                      88.3%
                                      NA18504.assemble_contigs
                                      8.0Kbp
                                      4.1Kbp
                                      98.2K
                                      216370.0K
                                      118.3Kbp
                                      2722.1Mbp
                                      1463.0
                                      107.57
                                      21.28
                                      88.3%
                                      NA18505.assemble_contigs
                                      8.1Kbp
                                      4.2Kbp
                                      97.1K
                                      213471.0K
                                      93.3Kbp
                                      2701.5Mbp
                                      1510.0
                                      108.11
                                      20.98
                                      87.7%
                                      NA19099.assemble_contigs
                                      8.5Kbp
                                      4.4Kbp
                                      92.2K
                                      202381.0K
                                      101.8Kbp
                                      2703.3Mbp
                                      1579.0
                                      107.98
                                      20.99
                                      87.8%
                                      NA19107.assemble_contigs
                                      9.3Kbp
                                      4.8Kbp
                                      85.6K
                                      188673.0K
                                      111.4Kbp
                                      2750.0Mbp
                                      1799.0
                                      110.58
                                      24.62
                                      89.0%
                                      NA19118.assemble_contigs
                                      8.4Kbp
                                      4.3Kbp
                                      93.3K
                                      204862.0K
                                      127.5Kbp
                                      2703.0Mbp
                                      1549.0
                                      107.68
                                      20.82
                                      87.8%
                                      NA19129.assemble_contigs
                                      10.8Kbp
                                      5.6Kbp
                                      73.9K
                                      161555.0K
                                      123.6Kbp
                                      2734.4Mbp
                                      1892.0
                                      111.13
                                      24.89
                                      88.7%
                                      NA19131.assemble_contigs
                                      12.0Kbp
                                      6.2Kbp
                                      66.2K
                                      145258.0K
                                      133.7Kbp
                                      2732.8Mbp
                                      1801.0
                                      111.39
                                      25.10
                                      88.7%
                                      PAV0Q.assemble_contigs
                                      6.7Kbp
                                      3.5Kbp
                                      116.2K
                                      254496.0K
                                      86.9Kbp
                                      2693.0Mbp
                                      648.0
                                      103.54
                                      20.49
                                      87.4%
                                      PAZ0V.assemble_contigs
                                      6.7Kbp
                                      3.5Kbp
                                      117.5K
                                      256264.0K
                                      102.2Kbp
                                      2677.5Mbp
                                      592.0
                                      103.41
                                      20.20
                                      86.9%
                                      PBA0X.assemble_contigs
                                      6.8Kbp
                                      3.5Kbp
                                      114.6K
                                      251112.0K
                                      82.7Kbp
                                      2692.6Mbp
                                      635.0
                                      103.68
                                      20.49
                                      87.4%
                                      PBC0A.assemble_contigs
                                      6.7Kbp
                                      3.5Kbp
                                      116.9K
                                      255057.0K
                                      80.9Kbp
                                      2677.5Mbp
                                      572.0
                                      103.63
                                      20.27
                                      86.9%
                                      SAMEA2580885.assemble_contigs
                                      4.9Kbp
                                      2.5Kbp
                                      161.9K
                                      355197.0K
                                      63.0Kbp
                                      2720.3Mbp
                                      1826.0
                                      108.65
                                      20.14
                                      87.7%
                                      SAMEA2580886.assemble_contigs
                                      5.8Kbp
                                      3.0Kbp
                                      135.7K
                                      296941.0K
                                      83.8Kbp
                                      2719.7Mbp
                                      1736.0
                                      108.34
                                      20.19
                                      88.0%
                                      SAMEA2580889.assemble_contigs
                                      5.8Kbp
                                      3.0Kbp
                                      135.4K
                                      295658.0K
                                      87.6Kbp
                                      2714.4Mbp
                                      1714.0
                                      107.94
                                      19.88
                                      87.9%
                                      SAMEA2580891.assemble_contigs
                                      5.9Kbp
                                      3.1Kbp
                                      133.3K
                                      290898.0K
                                      74.3Kbp
                                      2699.9Mbp
                                      1598.0
                                      108.18
                                      19.95
                                      87.4%
                                      SAMEA2580897.assemble_contigs
                                      7.9Kbp
                                      4.0Kbp
                                      98.5K
                                      218360.0K
                                      109.4Kbp
                                      2726.5Mbp
                                      1412.0
                                      107.25
                                      24.01
                                      88.1%
                                      SAMEA3506075.assemble_contigs
                                      10.1Kbp
                                      5.2Kbp
                                      78.2K
                                      172292.0K
                                      122.5Kbp
                                      2739.4Mbp
                                      1470.0
                                      108.36
                                      24.30
                                      88.8%
                                      SAMEA3506076.assemble_contigs
                                      10.8Kbp
                                      5.5Kbp
                                      72.7K
                                      160547.0K
                                      130.5Kbp
                                      2722.1Mbp
                                      1406.0
                                      108.36
                                      24.36
                                      88.3%
                                      SAMEA3506077.assemble_contigs
                                      9.2Kbp
                                      4.7Kbp
                                      86.3K
                                      190186.0K
                                      108.3Kbp
                                      2740.3Mbp
                                      1478.0
                                      108.28
                                      24.19
                                      88.8%
                                      SAMEA3506078.assemble_contigs
                                      7.6Kbp
                                      3.9Kbp
                                      102.9K
                                      229398.0K
                                      111.6Kbp
                                      2741.2Mbp
                                      1423.0
                                      107.91
                                      23.84
                                      88.6%
                                      + +
                                      + +
                                      +
                                      + + + + +
                                      + +

                                      + Number of Contigs + +

                                      + +

                                      This plot shows the number of contigs found for each assembly, broken + down by length.

                                      + + +
                                      + + +
                                      +
                                      loading..
                                      +
                                      + + +
                                      + + +
                                      +
                                      + + + +
                                      +

                                      BUSCO

                                      +

                                      BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

                                      + + + + +
                                      + +

                                      + Lineage: eukaryota_odb10 + +

                                      + + + + +
                                      + + +
                                      +
                                      loading..
                                      +
                                      + + +
                                      + + +
                                      + + + + +
                                      + +
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                                      + + +

                                      + + + + + MultiQC v1.9 + + - Written by Phil Ewels, + available on GitHub. +

                                      +

                                      + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                            + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                            + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                            + Bioinformatics (2016)
                                            + doi: 10.1093/bioinformatics/btw354
                                            + PMID: 27312411 +
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                                            About MultiQC

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                                            This report was generated using MultiQC, version 1.9

                                            +

                                            You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

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                                            For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

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                                            You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

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                                            MultiQC is published in Bioinformatics:

                                            +
                                            + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                            + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                            + Bioinformatics (2016)
                                            + doi: 10.1093/bioinformatics/btw354
                                            + PMID: 27312411 +
                                            +
                                            + +
                                            + +
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                                            + + + + +

                                            + + + +

                                            + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                            + + + + + + + + + + + +
                                            +

                                            Report + + generated on 2022-03-30, 11:11 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/KhoeSan

                                            + + +
                                            + + + + + + + +
                                            + + + + + + + + +
                                            +

                                            General Statistics

                                            + + + + + + + + + + Showing 32/32 rows and 2/2 columns. + +
                                            +
                                            + +
                                            Sample NameN50 (Kbp)Length (Mbp)
                                            KSP062.assemble_contigs
                                            2.2Kbp
                                            2492.7Mbp
                                            KSP063.assemble_contigs
                                            1.7Kbp
                                            2468.8Mbp
                                            KSP065.assemble_contigs
                                            2.2Kbp
                                            2506.1Mbp
                                            KSP067.assemble_contigs
                                            2.0Kbp
                                            2444.3Mbp
                                            KSP069.assemble_contigs
                                            2.3Kbp
                                            2503.4Mbp
                                            KSP092.assemble_contigs
                                            2.3Kbp
                                            2517.1Mbp
                                            KSP096.assemble_contigs
                                            1.7Kbp
                                            2445.2Mbp
                                            KSP103.assemble_contigs
                                            1.8Kbp
                                            2383.6Mbp
                                            KSP105.assemble_contigs
                                            2.0Kbp
                                            2400.3Mbp
                                            KSP106.assemble_contigs
                                            2.1Kbp
                                            2456.8Mbp
                                            KSP111.assemble_contigs
                                            2.2Kbp
                                            2479.9Mbp
                                            KSP116.assemble_contigs
                                            2.5Kbp
                                            2530.2Mbp
                                            KSP124.assemble_contigs
                                            1.4Kbp
                                            2300.2Mbp
                                            KSP134.assemble_contigs
                                            2.2Kbp
                                            2508.1Mbp
                                            KSP137.assemble_contigs
                                            2.0Kbp
                                            2477.1Mbp
                                            KSP139.assemble_contigs
                                            2.6Kbp
                                            2549.4Mbp
                                            KSP140.assemble_contigs
                                            2.4Kbp
                                            2525.9Mbp
                                            KSP146.assemble_contigs
                                            2.5Kbp
                                            2528.9Mbp
                                            KSP150.assemble_contigs
                                            2.2Kbp
                                            2513.6Mbp
                                            KSP152.assemble_contigs
                                            2.2Kbp
                                            2528.4Mbp
                                            KSP154.assemble_contigs
                                            2.3Kbp
                                            2533.6Mbp
                                            KSP155.assemble_contigs
                                            2.3Kbp
                                            2530.8Mbp
                                            KSP224.assemble_contigs
                                            2.4Kbp
                                            2554.3Mbp
                                            KSP225.assemble_contigs
                                            2.4Kbp
                                            2544.6Mbp
                                            KSP228.assemble_contigs
                                            2.3Kbp
                                            2534.6Mbp
                                            LP6005441_DNA_A11.assemble_contigs
                                            0.9Kbp
                                            1568.7Mbp
                                            LP6005441_DNA_B11.assemble_contigs
                                            0.8Kbp
                                            1367.4Mbp
                                            LP6005443_DNA_G08.assemble_contigs
                                            1.2Kbp
                                            2150.8Mbp
                                            LP6005592_DNA_C05.assemble_contigs
                                            1.4Kbp
                                            2324.5Mbp
                                            LP6005677_DNA_D03.assemble_contigs
                                            1.3Kbp
                                            2239.1Mbp
                                            SAMEA2580840.assemble_contigs
                                            5.2Kbp
                                            2698.9Mbp
                                            SAMEA2580841.assemble_contigs
                                            8.5Kbp
                                            2735.1Mbp
                                            + + +
                                            + + + + + + +
                                            +

                                            QUAST

                                            +

                                            QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                            + + + + +
                                            + +

                                            + Assembly Statistics + +

                                            + + + + +
                                            + + + + + + + + + Showing 32/32 rows and 10/10 columns. + +
                                            +
                                            + +
                                            Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                            KSP062.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            320.5K
                                            705777.0K
                                            39.5Kbp
                                            2492.7Mbp
                                            2376.0
                                            108.32
                                            17.11
                                            79.9%
                                            KSP063.assemble_contigs
                                            1.7Kbp
                                            1.0Kbp
                                            444.6K
                                            927421.0K
                                            34.2Kbp
                                            2468.8Mbp
                                            10666.0
                                            108.06
                                            17.49
                                            78.6%
                                            KSP065.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            316.2K
                                            693311.0K
                                            46.7Kbp
                                            2506.1Mbp
                                            2587.0
                                            106.93
                                            17.04
                                            80.3%
                                            KSP067.assemble_contigs
                                            2.0Kbp
                                            1.1Kbp
                                            351.5K
                                            768475.0K
                                            42.8Kbp
                                            2444.3Mbp
                                            2189.0
                                            105.76
                                            17.07
                                            78.3%
                                            KSP069.assemble_contigs
                                            2.3Kbp
                                            1.2Kbp
                                            309.7K
                                            687681.0K
                                            42.5Kbp
                                            2503.4Mbp
                                            2061.0
                                            108.16
                                            17.27
                                            80.3%
                                            KSP092.assemble_contigs
                                            2.3Kbp
                                            1.2Kbp
                                            316.3K
                                            692162.0K
                                            39.0Kbp
                                            2517.1Mbp
                                            2560.0
                                            107.87
                                            17.37
                                            80.7%
                                            KSP096.assemble_contigs
                                            1.7Kbp
                                            1.0Kbp
                                            419.9K
                                            884356.0K
                                            26.8Kbp
                                            2445.2Mbp
                                            7358.0
                                            106.03
                                            17.17
                                            78.0%
                                            KSP103.assemble_contigs
                                            1.8Kbp
                                            1.1Kbp
                                            383.6K
                                            817438.0K
                                            25.9Kbp
                                            2383.6Mbp
                                            6297.0
                                            108.18
                                            17.43
                                            76.1%
                                            KSP105.assemble_contigs
                                            2.0Kbp
                                            1.1Kbp
                                            340.8K
                                            751339.0K
                                            41.0Kbp
                                            2400.3Mbp
                                            2763.0
                                            107.78
                                            17.19
                                            76.9%
                                            KSP106.assemble_contigs
                                            2.1Kbp
                                            1.2Kbp
                                            335.5K
                                            731415.0K
                                            32.0Kbp
                                            2456.8Mbp
                                            3772.0
                                            109.42
                                            17.17
                                            78.7%
                                            KSP111.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            307.0K
                                            685890.0K
                                            41.6Kbp
                                            2479.9Mbp
                                            2332.0
                                            109.41
                                            17.40
                                            79.6%
                                            KSP116.assemble_contigs
                                            2.5Kbp
                                            1.3Kbp
                                            279.9K
                                            628835.0K
                                            59.0Kbp
                                            2530.2Mbp
                                            2030.0
                                            110.40
                                            17.36
                                            81.3%
                                            KSP124.assemble_contigs
                                            1.4Kbp
                                            0.9Kbp
                                            511.8K
                                            1040794.0K
                                            27.0Kbp
                                            2300.2Mbp
                                            21513.0
                                            103.22
                                            16.55
                                            73.0%
                                            KSP134.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            318.1K
                                            697214.0K
                                            40.7Kbp
                                            2508.1Mbp
                                            2803.0
                                            105.88
                                            16.68
                                            80.4%
                                            KSP137.assemble_contigs
                                            2.0Kbp
                                            1.1Kbp
                                            351.4K
                                            762298.0K
                                            41.3Kbp
                                            2477.1Mbp
                                            3703.0
                                            104.93
                                            16.79
                                            79.3%
                                            KSP139.assemble_contigs
                                            2.6Kbp
                                            1.4Kbp
                                            270.6K
                                            609036.0K
                                            49.9Kbp
                                            2549.4Mbp
                                            1908.0
                                            107.40
                                            17.14
                                            82.0%
                                            KSP140.assemble_contigs
                                            2.4Kbp
                                            1.3Kbp
                                            290.7K
                                            649068.0K
                                            44.7Kbp
                                            2525.9Mbp
                                            2058.0
                                            106.49
                                            16.81
                                            81.1%
                                            KSP146.assemble_contigs
                                            2.5Kbp
                                            1.3Kbp
                                            283.6K
                                            634573.0K
                                            48.4Kbp
                                            2528.9Mbp
                                            1879.0
                                            107.57
                                            16.96
                                            81.3%
                                            KSP150.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            313.4K
                                            698336.0K
                                            175.9Kbp
                                            2513.6Mbp
                                            2477.0
                                            106.99
                                            17.16
                                            79.9%
                                            KSP152.assemble_contigs
                                            2.2Kbp
                                            1.2Kbp
                                            324.0K
                                            710087.0K
                                            38.7Kbp
                                            2528.4Mbp
                                            2808.0
                                            107.26
                                            17.24
                                            81.0%
                                            KSP154.assemble_contigs
                                            2.3Kbp
                                            1.3Kbp
                                            302.9K
                                            675867.0K
                                            57.5Kbp
                                            2533.6Mbp
                                            2517.0
                                            107.69
                                            17.18
                                            81.1%
                                            KSP155.assemble_contigs
                                            2.3Kbp
                                            1.3Kbp
                                            310.8K
                                            686260.0K
                                            41.8Kbp
                                            2530.8Mbp
                                            2475.0
                                            107.36
                                            17.29
                                            81.1%
                                            KSP224.assemble_contigs
                                            2.4Kbp
                                            1.3Kbp
                                            300.7K
                                            661178.0K
                                            63.9Kbp
                                            2554.3Mbp
                                            1794.0
                                            108.13
                                            17.27
                                            81.9%
                                            KSP225.assemble_contigs
                                            2.4Kbp
                                            1.3Kbp
                                            294.4K
                                            650219.0K
                                            53.0Kbp
                                            2544.6Mbp
                                            1698.0
                                            108.47
                                            17.25
                                            81.7%
                                            KSP228.assemble_contigs
                                            2.3Kbp
                                            1.2Kbp
                                            316.0K
                                            696109.0K
                                            46.1Kbp
                                            2534.6Mbp
                                            1965.0
                                            106.59
                                            17.39
                                            81.2%
                                            LP6005441_DNA_A11.assemble_contigs
                                            0.9Kbp
                                            0.7Kbp
                                            625.2K
                                            1148198.0K
                                            13.3Kbp
                                            1568.7Mbp
                                            661.0
                                            87.31
                                            12.99
                                            50.3%
                                            LP6005441_DNA_B11.assemble_contigs
                                            0.8Kbp
                                            0.6Kbp
                                            607.0K
                                            1091469.0K
                                            11.3Kbp
                                            1367.4Mbp
                                            577.0
                                            85.87
                                            12.66
                                            43.9%
                                            LP6005443_DNA_G08.assemble_contigs
                                            1.2Kbp
                                            0.8Kbp
                                            535.2K
                                            1076745.0K
                                            30.3Kbp
                                            2150.8Mbp
                                            1404.0
                                            96.50
                                            15.53
                                            68.7%
                                            LP6005592_DNA_C05.assemble_contigs
                                            1.4Kbp
                                            0.9Kbp
                                            501.6K
                                            1037828.0K
                                            81.3Kbp
                                            2324.5Mbp
                                            1369.0
                                            97.55
                                            15.94
                                            73.6%
                                            LP6005677_DNA_D03.assemble_contigs
                                            1.3Kbp
                                            0.8Kbp
                                            521.5K
                                            1063718.0K
                                            71.9Kbp
                                            2239.1Mbp
                                            1270.0
                                            98.11
                                            15.49
                                            71.3%
                                            SAMEA2580840.assemble_contigs
                                            5.2Kbp
                                            2.7Kbp
                                            149.8K
                                            327050.0K
                                            76.0Kbp
                                            2698.9Mbp
                                            1744.0
                                            119.06
                                            19.98
                                            87.4%
                                            SAMEA2580841.assemble_contigs
                                            8.5Kbp
                                            4.3Kbp
                                            92.4K
                                            204737.0K
                                            294.6Kbp
                                            2735.1Mbp
                                            1439.0
                                            118.90
                                            26.25
                                            88.3%
                                            + +
                                            + +
                                            +
                                            + + + + +
                                            + +

                                            + Number of Contigs + +

                                            + +

                                            This plot shows the number of contigs found for each assembly, broken + down by length.

                                            + + +
                                            + + +
                                            +
                                            loading..
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                                            + + + + + MultiQC v1.9 + + - Written by Phil Ewels, + available on GitHub. +

                                            +

                                            + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                            + + + + + + + + + + + + + + From 2234bf46e1ee470499f8f6ade3d98cec91a39f80 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:31:37 +0200 Subject: [PATCH 17/28] Added MultiQC files of final dataset --- .../multiQC/finalDataset/BantuNC_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/CARF_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/CWNC_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/EAAA_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/EANS_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/FWNC_report.html | 6068 +++++++++++++++++ .../multiQC/finalDataset/KS_report.html | 6068 +++++++++++++++++ 7 files changed, 42476 insertions(+) create mode 100644 dataAnalysis/multiQC/finalDataset/BantuNC_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/CARF_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/CWNC_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/EAAA_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/EANS_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/FWNC_report.html create mode 100644 dataAnalysis/multiQC/finalDataset/KS_report.html diff --git a/dataAnalysis/multiQC/finalDataset/BantuNC_report.html b/dataAnalysis/multiQC/finalDataset/BantuNC_report.html new file mode 100644 index 0000000..1ea1c75 --- /dev/null +++ b/dataAnalysis/multiQC/finalDataset/BantuNC_report.html @@ -0,0 +1,6068 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                                                  + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                  + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                  + Bioinformatics (2016)
                                                  + doi: 10.1093/bioinformatics/btw354
                                                  + PMID: 27312411 +
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                                                  About MultiQC

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                                                  This report was generated using MultiQC, version 1.12

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                                                  You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

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                                                  For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

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                                                  You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                  +

                                                  MultiQC is published in Bioinformatics:

                                                  +
                                                  + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                  + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                  + Bioinformatics (2016)
                                                  + doi: 10.1093/bioinformatics/btw354
                                                  + PMID: 27312411 +
                                                  +
                                                  + +
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                                                  + + + +

                                                  + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

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                                                  +

                                                  Report + + generated on 2022-02-15, 04:21 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/BantuNC/logs/f9/ba543ed80482b3e6a815c43ab8edd7

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                                                  +

                                                  General Statistics

                                                  + + + + + + + + + + + Showing 35/35 rows and 2/2 columns. + +
                                                  +
                                                  + +
                                                  Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                  LP6005441_DNA_F01.assemble_contigs
                                                  1.1Kbp
                                                  1957.2Mbp
                                                  LP6005443_DNA_A01.assemble_contigs
                                                  1.3Kbp
                                                  2182.1Mbp
                                                  LP6005443_DNA_E02.assemble_contigs
                                                  1.2Kbp
                                                  2111.6Mbp
                                                  LP6005443_DNA_G02.assemble_contigs
                                                  1.1Kbp
                                                  2006.5Mbp
                                                  NA19028.assemble_contigs
                                                  8.0Kbp
                                                  2719.7Mbp
                                                  NA19038.assemble_contigs
                                                  8.2Kbp
                                                  2703.8Mbp
                                                  NA19309.assemble_contigs
                                                  8.4Kbp
                                                  2751.0Mbp
                                                  NA19317.assemble_contigs
                                                  8.4Kbp
                                                  2721.0Mbp
                                                  NA19318.assemble_contigs
                                                  11.0Kbp
                                                  2749.5Mbp
                                                  NA19328.assemble_contigs
                                                  12.3Kbp
                                                  2729.4Mbp
                                                  NA19332.assemble_contigs
                                                  8.5Kbp
                                                  2706.5Mbp
                                                  NA19350.assemble_contigs
                                                  7.8Kbp
                                                  2720.1Mbp
                                                  NA19372.assemble_contigs
                                                  9.8Kbp
                                                  2749.7Mbp
                                                  NA19380.assemble_contigs
                                                  7.9Kbp
                                                  2719.0Mbp
                                                  NA19385.assemble_contigs
                                                  8.1Kbp
                                                  2721.1Mbp
                                                  NA19434.assemble_contigs
                                                  9.9Kbp
                                                  2732.8Mbp
                                                  NA19448.assemble_contigs
                                                  9.5Kbp
                                                  2750.4Mbp
                                                  NA19461.assemble_contigs
                                                  9.8Kbp
                                                  2751.1Mbp
                                                  NA19463.assemble_contigs
                                                  8.2Kbp
                                                  2708.0Mbp
                                                  NA19467.assemble_contigs
                                                  9.7Kbp
                                                  2736.1Mbp
                                                  NA19471.assemble_contigs
                                                  9.5Kbp
                                                  2737.2Mbp
                                                  NA19473.assemble_contigs
                                                  9.2Kbp
                                                  2737.4Mbp
                                                  SAMEA2580844.assemble_contigs
                                                  6.1Kbp
                                                  2716.4Mbp
                                                  SAMEA2580845.assemble_contigs
                                                  5.6Kbp
                                                  2709.8Mbp
                                                  SAMEA2580848.assemble_contigs
                                                  5.8Kbp
                                                  2712.7Mbp
                                                  SAMEA2580849.assemble_contigs
                                                  9.5Kbp
                                                  2730.6Mbp
                                                  SAMEA2580852.assemble_contigs
                                                  5.8Kbp
                                                  2712.1Mbp
                                                  SAMEA2580853.assemble_contigs
                                                  5.7Kbp
                                                  2712.8Mbp
                                                  SAMEA2580854.assemble_contigs
                                                  5.9Kbp
                                                  2713.3Mbp
                                                  SAMEA2580855.assemble_contigs
                                                  6.0Kbp
                                                  2715.6Mbp
                                                  SAMEA2580856.assemble_contigs
                                                  5.7Kbp
                                                  2716.2Mbp
                                                  SAMEA2580858.assemble_contigs
                                                  2.0Kbp
                                                  2522.0Mbp
                                                  SAMEA2580859.assemble_contigs
                                                  3.9Kbp
                                                  2691.3Mbp
                                                  SAMEA2580861.assemble_contigs
                                                  2.1Kbp
                                                  2548.3Mbp
                                                  SAMEA2580862.assemble_contigs
                                                  2.0Kbp
                                                  2506.8Mbp
                                                  + + +
                                                  + + + + + + +
                                                  + + +
                                                  +

                                                  QUAST

                                                  +

                                                  QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                  + + + + +
                                                  + +

                                                  + Assembly Statistics + +

                                                  + + + + +
                                                  + + + + + + + + + Showing 35/35 rows and 10/10 columns. + +
                                                  +
                                                  + +
                                                  Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                  LP6005441_DNA_F01.assemble_contigs
                                                  1.1Kbp
                                                  0.7Kbp
                                                  600.4K
                                                  1159.4K
                                                  11.9Kbp
                                                  1957.2Mbp
                                                  1030.0
                                                  82.73
                                                  13.15
                                                  62.5%
                                                  LP6005443_DNA_A01.assemble_contigs
                                                  1.3Kbp
                                                  0.8Kbp
                                                  512.1K
                                                  1043.4K
                                                  20.6Kbp
                                                  2182.1Mbp
                                                  1279.0
                                                  85.30
                                                  13.89
                                                  69.7%
                                                  LP6005443_DNA_E02.assemble_contigs
                                                  1.2Kbp
                                                  0.8Kbp
                                                  544.7K
                                                  1088.8K
                                                  23.9Kbp
                                                  2111.6Mbp
                                                  1209.0
                                                  85.25
                                                  14.03
                                                  67.4%
                                                  LP6005443_DNA_G02.assemble_contigs
                                                  1.1Kbp
                                                  0.8Kbp
                                                  570.5K
                                                  1120.9K
                                                  16.6Kbp
                                                  2006.5Mbp
                                                  973.0
                                                  85.70
                                                  13.81
                                                  64.1%
                                                  NA19028.assemble_contigs
                                                  8.0Kbp
                                                  4.1Kbp
                                                  97.7K
                                                  214.8K
                                                  113.8Kbp
                                                  2719.7Mbp
                                                  1547.0
                                                  107.83
                                                  21.03
                                                  88.3%
                                                  NA19038.assemble_contigs
                                                  8.2Kbp
                                                  4.2Kbp
                                                  95.3K
                                                  210.0K
                                                  118.3Kbp
                                                  2703.8Mbp
                                                  1474.0
                                                  107.51
                                                  21.06
                                                  87.8%
                                                  NA19309.assemble_contigs
                                                  8.4Kbp
                                                  4.3Kbp
                                                  93.7K
                                                  206.8K
                                                  115.6Kbp
                                                  2751.0Mbp
                                                  1912.0
                                                  110.33
                                                  24.37
                                                  89.0%
                                                  NA19317.assemble_contigs
                                                  8.4Kbp
                                                  4.3Kbp
                                                  93.0K
                                                  205.0K
                                                  106.1Kbp
                                                  2721.0Mbp
                                                  1600.0
                                                  107.81
                                                  21.14
                                                  88.4%
                                                  NA19318.assemble_contigs
                                                  11.0Kbp
                                                  5.7Kbp
                                                  73.0K
                                                  159.6K
                                                  129.2Kbp
                                                  2749.5Mbp
                                                  1901.0
                                                  110.76
                                                  25.07
                                                  89.2%
                                                  NA19328.assemble_contigs
                                                  12.3Kbp
                                                  6.3Kbp
                                                  64.3K
                                                  141.2K
                                                  143.3Kbp
                                                  2729.4Mbp
                                                  1833.0
                                                  111.62
                                                  24.98
                                                  88.6%
                                                  NA19332.assemble_contigs
                                                  8.5Kbp
                                                  4.4Kbp
                                                  92.4K
                                                  203.3K
                                                  102.1Kbp
                                                  2706.5Mbp
                                                  1610.0
                                                  107.74
                                                  21.15
                                                  87.9%
                                                  NA19350.assemble_contigs
                                                  7.8Kbp
                                                  4.0Kbp
                                                  100.2K
                                                  220.7K
                                                  95.2Kbp
                                                  2720.1Mbp
                                                  1580.0
                                                  107.41
                                                  21.03
                                                  88.3%
                                                  NA19372.assemble_contigs
                                                  9.8Kbp
                                                  5.0Kbp
                                                  81.2K
                                                  178.9K
                                                  151.6Kbp
                                                  2749.7Mbp
                                                  1896.0
                                                  111.22
                                                  24.84
                                                  89.1%
                                                  NA19380.assemble_contigs
                                                  7.9Kbp
                                                  4.1Kbp
                                                  99.1K
                                                  218.0K
                                                  100.3Kbp
                                                  2719.0Mbp
                                                  1522.0
                                                  107.32
                                                  21.02
                                                  88.2%
                                                  NA19385.assemble_contigs
                                                  8.1Kbp
                                                  4.2Kbp
                                                  97.0K
                                                  213.5K
                                                  129.6Kbp
                                                  2721.1Mbp
                                                  1571.0
                                                  107.94
                                                  21.15
                                                  88.3%
                                                  NA19434.assemble_contigs
                                                  9.9Kbp
                                                  5.1Kbp
                                                  80.3K
                                                  176.5K
                                                  118.9Kbp
                                                  2732.8Mbp
                                                  1785.0
                                                  109.77
                                                  24.53
                                                  88.5%
                                                  NA19448.assemble_contigs
                                                  9.5Kbp
                                                  4.9Kbp
                                                  83.2K
                                                  183.6K
                                                  132.2Kbp
                                                  2750.4Mbp
                                                  1947.0
                                                  111.19
                                                  24.72
                                                  89.1%
                                                  NA19461.assemble_contigs
                                                  9.8Kbp
                                                  5.1Kbp
                                                  81.5K
                                                  178.7K
                                                  114.8Kbp
                                                  2751.1Mbp
                                                  1891.0
                                                  110.49
                                                  24.73
                                                  89.1%
                                                  NA19463.assemble_contigs
                                                  8.2Kbp
                                                  4.2Kbp
                                                  95.9K
                                                  210.7K
                                                  158.2Kbp
                                                  2708.0Mbp
                                                  1628.0
                                                  108.24
                                                  21.00
                                                  87.9%
                                                  NA19467.assemble_contigs
                                                  9.7Kbp
                                                  5.0Kbp
                                                  81.3K
                                                  178.7K
                                                  134.5Kbp
                                                  2736.1Mbp
                                                  1958.0
                                                  110.66
                                                  24.60
                                                  88.6%
                                                  NA19471.assemble_contigs
                                                  9.5Kbp
                                                  4.9Kbp
                                                  84.1K
                                                  183.9K
                                                  120.4Kbp
                                                  2737.2Mbp
                                                  1952.0
                                                  111.47
                                                  24.82
                                                  88.6%
                                                  NA19473.assemble_contigs
                                                  9.2Kbp
                                                  4.8Kbp
                                                  86.0K
                                                  188.1K
                                                  121.2Kbp
                                                  2737.4Mbp
                                                  1836.0
                                                  110.59
                                                  24.72
                                                  88.6%
                                                  SAMEA2580844.assemble_contigs
                                                  6.1Kbp
                                                  3.2Kbp
                                                  130.0K
                                                  283.5K
                                                  79.3Kbp
                                                  2716.4Mbp
                                                  1575.0
                                                  111.19
                                                  20.63
                                                  87.9%
                                                  SAMEA2580845.assemble_contigs
                                                  5.6Kbp
                                                  2.9Kbp
                                                  141.3K
                                                  308.6K
                                                  72.4Kbp
                                                  2709.8Mbp
                                                  1613.0
                                                  110.68
                                                  19.81
                                                  87.7%
                                                  SAMEA2580848.assemble_contigs
                                                  5.8Kbp
                                                  3.0Kbp
                                                  136.1K
                                                  297.5K
                                                  83.7Kbp
                                                  2712.7Mbp
                                                  1670.0
                                                  109.22
                                                  19.60
                                                  87.8%
                                                  SAMEA2580849.assemble_contigs
                                                  9.5Kbp
                                                  4.8Kbp
                                                  82.6K
                                                  183.4K
                                                  118.6Kbp
                                                  2730.6Mbp
                                                  1491.0
                                                  110.00
                                                  24.33
                                                  88.4%
                                                  SAMEA2580852.assemble_contigs
                                                  5.8Kbp
                                                  3.0Kbp
                                                  135.9K
                                                  296.7K
                                                  81.3Kbp
                                                  2712.1Mbp
                                                  1581.0
                                                  108.18
                                                  19.49
                                                  87.8%
                                                  SAMEA2580853.assemble_contigs
                                                  5.7Kbp
                                                  3.0Kbp
                                                  138.4K
                                                  302.0K
                                                  76.7Kbp
                                                  2712.8Mbp
                                                  1632.0
                                                  108.50
                                                  19.47
                                                  87.8%
                                                  SAMEA2580854.assemble_contigs
                                                  5.9Kbp
                                                  3.1Kbp
                                                  134.3K
                                                  293.5K
                                                  82.7Kbp
                                                  2713.3Mbp
                                                  1702.0
                                                  108.29
                                                  19.58
                                                  87.9%
                                                  SAMEA2580855.assemble_contigs
                                                  6.0Kbp
                                                  3.1Kbp
                                                  132.4K
                                                  288.8K
                                                  74.6Kbp
                                                  2715.6Mbp
                                                  1694.0
                                                  107.96
                                                  19.53
                                                  87.9%
                                                  SAMEA2580856.assemble_contigs
                                                  5.7Kbp
                                                  3.0Kbp
                                                  137.9K
                                                  302.0K
                                                  74.1Kbp
                                                  2716.2Mbp
                                                  1613.0
                                                  107.93
                                                  19.73
                                                  87.9%
                                                  SAMEA2580858.assemble_contigs
                                                  2.0Kbp
                                                  1.1Kbp
                                                  372.8K
                                                  791.7K
                                                  35.8Kbp
                                                  2522.0Mbp
                                                  1391.0
                                                  103.45
                                                  15.93
                                                  80.4%
                                                  SAMEA2580859.assemble_contigs
                                                  3.9Kbp
                                                  2.0Kbp
                                                  200.2K
                                                  439.3K
                                                  73.7Kbp
                                                  2691.3Mbp
                                                  1697.0
                                                  105.49
                                                  18.13
                                                  86.6%
                                                  SAMEA2580861.assemble_contigs
                                                  2.1Kbp
                                                  1.2Kbp
                                                  353.1K
                                                  752.6K
                                                  29.3Kbp
                                                  2548.3Mbp
                                                  1435.0
                                                  104.40
                                                  15.76
                                                  81.4%
                                                  SAMEA2580862.assemble_contigs
                                                  2.0Kbp
                                                  1.1Kbp
                                                  375.1K
                                                  796.0K
                                                  36.7Kbp
                                                  2506.8Mbp
                                                  1423.0
                                                  104.43
                                                  15.59
                                                  80.0%
                                                  + +
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                                                  + +

                                                  + Number of Contigs + +

                                                  + +

                                                  This plot shows the number of contigs found for each assembly, broken + down by length.

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                                                  loading..
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                                                  BUSCO

                                                  +

                                                  BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                  + + + + +
                                                  + +

                                                  + Lineage: eukaryota_odb10 + +

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                                                  + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                  +

                                                  + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                                        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                        + Bioinformatics (2016)
                                                        + doi: 10.1093/bioinformatics/btw354
                                                        + PMID: 27312411 +
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                                                        About MultiQC

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                                                        This report was generated using MultiQC, version 1.12

                                                        +

                                                        You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

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                                                        For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                        +

                                                        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                        +

                                                        MultiQC is published in Bioinformatics:

                                                        +
                                                        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                        + Bioinformatics (2016)
                                                        + doi: 10.1093/bioinformatics/btw354
                                                        + PMID: 27312411 +
                                                        +
                                                        + +
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                                                        + + + +

                                                        + + + + +

                                                        + + + +

                                                        + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                        + + + + + + + + + + + +
                                                        +

                                                        Report + + generated on 2022-02-15, 04:06 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/CARF/logs/a0/1ba21958406cff81a43994c1c29682

                                                        + + +
                                                        + + + + + + + +
                                                        + + + + + + + + +
                                                        +

                                                        General Statistics

                                                        + + + + + + + + + + + Showing 22/22 rows and 2/2 columns. + +
                                                        +
                                                        + +
                                                        Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                        LP6005441_DNA_G02.assemble_contigs
                                                        1.1Kbp
                                                        2060.9Mbp
                                                        LP6005441_DNA_H02.assemble_contigs
                                                        1.1Kbp
                                                        2057.6Mbp
                                                        LP6005592_DNA_C03.assemble_contigs
                                                        1.1Kbp
                                                        1963.4Mbp
                                                        SAMEA2580802.assemble_contigs
                                                        3.9Kbp
                                                        2697.1Mbp
                                                        SAMEA2580803.assemble_contigs
                                                        5.9Kbp
                                                        2713.1Mbp
                                                        SAMEA2580807.assemble_contigs
                                                        5.9Kbp
                                                        2712.8Mbp
                                                        SAMEA2580809.assemble_contigs
                                                        9.2Kbp
                                                        2737.4Mbp
                                                        SAMEA2580813.assemble_contigs
                                                        5.7Kbp
                                                        2713.8Mbp
                                                        SAMEA2580815.assemble_contigs
                                                        4.3Kbp
                                                        2703.7Mbp
                                                        SAMEA2580816.assemble_contigs
                                                        5.1Kbp
                                                        2688.7Mbp
                                                        SAMEA2580818.assemble_contigs
                                                        5.6Kbp
                                                        2684.2Mbp
                                                        SAMEA2580819.assemble_contigs
                                                        5.5Kbp
                                                        2688.3Mbp
                                                        SAMEA2580820.assemble_contigs
                                                        5.4Kbp
                                                        2688.1Mbp
                                                        SAMEA2580821.assemble_contigs
                                                        3.5Kbp
                                                        2692.6Mbp
                                                        SAMEA2580822.assemble_contigs
                                                        5.8Kbp
                                                        2704.2Mbp
                                                        SAMEA2580823.assemble_contigs
                                                        5.0Kbp
                                                        2703.5Mbp
                                                        SAMEA2580830.assemble_contigs
                                                        5.8Kbp
                                                        2704.0Mbp
                                                        SAMEA2580831.assemble_contigs
                                                        6.0Kbp
                                                        2699.3Mbp
                                                        SAMEA2580834.assemble_contigs
                                                        5.8Kbp
                                                        2703.3Mbp
                                                        SAMEA2580836.assemble_contigs
                                                        5.8Kbp
                                                        2703.9Mbp
                                                        SAMEA3506072.assemble_contigs
                                                        9.2Kbp
                                                        2737.7Mbp
                                                        SAMEA3506073.assemble_contigs
                                                        7.8Kbp
                                                        2708.6Mbp
                                                        + + +
                                                        + + + + + + +
                                                        + + +
                                                        +

                                                        QUAST

                                                        +

                                                        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                        + + + + +
                                                        + +

                                                        + Assembly Statistics + +

                                                        + + + + +
                                                        + + + + + + + + + Showing 22/22 rows and 10/10 columns. + +
                                                        +
                                                        + +
                                                        Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                        LP6005441_DNA_G02.assemble_contigs
                                                        1.1Kbp
                                                        0.8Kbp
                                                        573.5K
                                                        1127.4K
                                                        13.0Kbp
                                                        2060.9Mbp
                                                        1144.0
                                                        88.07
                                                        14.19
                                                        65.8%
                                                        LP6005441_DNA_H02.assemble_contigs
                                                        1.1Kbp
                                                        0.8Kbp
                                                        577.3K
                                                        1133.2K
                                                        17.3Kbp
                                                        2057.6Mbp
                                                        1198.0
                                                        88.37
                                                        14.18
                                                        65.7%
                                                        LP6005592_DNA_C03.assemble_contigs
                                                        1.1Kbp
                                                        0.7Kbp
                                                        594.5K
                                                        1150.1K
                                                        12.9Kbp
                                                        1963.4Mbp
                                                        1052.0
                                                        90.42
                                                        14.00
                                                        62.7%
                                                        SAMEA2580802.assemble_contigs
                                                        3.9Kbp
                                                        2.1Kbp
                                                        196.9K
                                                        432.3K
                                                        55.3Kbp
                                                        2697.1Mbp
                                                        1728.0
                                                        113.06
                                                        19.97
                                                        86.7%
                                                        SAMEA2580803.assemble_contigs
                                                        5.9Kbp
                                                        3.1Kbp
                                                        134.9K
                                                        294.0K
                                                        63.9Kbp
                                                        2713.1Mbp
                                                        1728.0
                                                        114.73
                                                        20.86
                                                        87.8%
                                                        SAMEA2580807.assemble_contigs
                                                        5.9Kbp
                                                        3.1Kbp
                                                        133.6K
                                                        291.5K
                                                        66.8Kbp
                                                        2712.8Mbp
                                                        1877.0
                                                        114.54
                                                        20.80
                                                        87.8%
                                                        SAMEA2580809.assemble_contigs
                                                        9.2Kbp
                                                        4.7Kbp
                                                        86.2K
                                                        189.8K
                                                        124.1Kbp
                                                        2737.4Mbp
                                                        1414.0
                                                        113.70
                                                        25.59
                                                        88.6%
                                                        SAMEA2580813.assemble_contigs
                                                        5.7Kbp
                                                        3.0Kbp
                                                        139.3K
                                                        303.6K
                                                        60.5Kbp
                                                        2713.8Mbp
                                                        1793.0
                                                        114.39
                                                        20.69
                                                        87.8%
                                                        SAMEA2580815.assemble_contigs
                                                        4.3Kbp
                                                        2.3Kbp
                                                        182.9K
                                                        399.0K
                                                        53.6Kbp
                                                        2703.7Mbp
                                                        1770.0
                                                        113.14
                                                        20.02
                                                        87.1%
                                                        SAMEA2580816.assemble_contigs
                                                        5.1Kbp
                                                        2.7Kbp
                                                        152.8K
                                                        333.2K
                                                        62.1Kbp
                                                        2688.7Mbp
                                                        1699.0
                                                        112.17
                                                        18.37
                                                        87.0%
                                                        SAMEA2580818.assemble_contigs
                                                        5.6Kbp
                                                        2.9Kbp
                                                        140.3K
                                                        306.5K
                                                        79.1Kbp
                                                        2684.2Mbp
                                                        1547.0
                                                        111.63
                                                        18.19
                                                        87.0%
                                                        SAMEA2580819.assemble_contigs
                                                        5.5Kbp
                                                        2.9Kbp
                                                        140.9K
                                                        308.1K
                                                        69.7Kbp
                                                        2688.3Mbp
                                                        1656.0
                                                        113.09
                                                        18.59
                                                        87.1%
                                                        SAMEA2580820.assemble_contigs
                                                        5.4Kbp
                                                        2.8Kbp
                                                        143.9K
                                                        314.4K
                                                        64.1Kbp
                                                        2688.1Mbp
                                                        1567.0
                                                        112.72
                                                        18.42
                                                        87.1%
                                                        SAMEA2580821.assemble_contigs
                                                        3.5Kbp
                                                        1.9Kbp
                                                        218.6K
                                                        478.2K
                                                        65.1Kbp
                                                        2692.6Mbp
                                                        1615.0
                                                        112.56
                                                        19.92
                                                        86.4%
                                                        SAMEA2580822.assemble_contigs
                                                        5.8Kbp
                                                        3.0Kbp
                                                        136.6K
                                                        298.3K
                                                        73.7Kbp
                                                        2704.2Mbp
                                                        1685.0
                                                        113.64
                                                        19.52
                                                        87.6%
                                                        SAMEA2580823.assemble_contigs
                                                        5.0Kbp
                                                        2.6Kbp
                                                        159.0K
                                                        346.5K
                                                        60.7Kbp
                                                        2703.5Mbp
                                                        1731.0
                                                        113.67
                                                        20.10
                                                        87.3%
                                                        SAMEA2580830.assemble_contigs
                                                        5.8Kbp
                                                        3.0Kbp
                                                        135.8K
                                                        296.6K
                                                        68.4Kbp
                                                        2704.0Mbp
                                                        1681.0
                                                        115.61
                                                        19.82
                                                        87.6%
                                                        SAMEA2580831.assemble_contigs
                                                        6.0Kbp
                                                        3.1Kbp
                                                        130.5K
                                                        284.7K
                                                        69.9Kbp
                                                        2699.3Mbp
                                                        1641.0
                                                        116.42
                                                        21.34
                                                        87.4%
                                                        SAMEA2580834.assemble_contigs
                                                        5.8Kbp
                                                        3.0Kbp
                                                        135.5K
                                                        296.0K
                                                        61.8Kbp
                                                        2703.3Mbp
                                                        1675.0
                                                        115.94
                                                        19.81
                                                        87.6%
                                                        SAMEA2580836.assemble_contigs
                                                        5.8Kbp
                                                        3.0Kbp
                                                        135.6K
                                                        296.2K
                                                        66.3Kbp
                                                        2703.9Mbp
                                                        1723.0
                                                        115.54
                                                        19.78
                                                        87.6%
                                                        SAMEA3506072.assemble_contigs
                                                        9.2Kbp
                                                        4.7Kbp
                                                        85.7K
                                                        188.9K
                                                        109.5Kbp
                                                        2737.7Mbp
                                                        1518.0
                                                        114.24
                                                        25.36
                                                        88.7%
                                                        SAMEA3506073.assemble_contigs
                                                        7.8Kbp
                                                        4.0Kbp
                                                        100.0K
                                                        221.2K
                                                        103.6Kbp
                                                        2708.6Mbp
                                                        1473.0
                                                        112.68
                                                        22.13
                                                        87.9%
                                                        + +
                                                        + + +
                                                        +
                                                        + + +
                                                        + + + + + +
                                                        + +

                                                        + Number of Contigs + +

                                                        + +

                                                        This plot shows the number of contigs found for each assembly, broken + down by length.

                                                        + + +
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                                                        +
                                                        loading..
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                                                        +

                                                        BUSCO

                                                        +

                                                        BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                        + + + + +
                                                        + +

                                                        + Lineage: eukaryota_odb10 + +

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                                                        loading..
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                                                        + + +

                                                        + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                        +

                                                        + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                                        + + + + + + + + + + + + + + diff --git a/dataAnalysis/multiQC/finalDataset/CWNC_report.html b/dataAnalysis/multiQC/finalDataset/CWNC_report.html new file mode 100644 index 0000000..4aba326 --- /dev/null +++ b/dataAnalysis/multiQC/finalDataset/CWNC_report.html @@ -0,0 +1,6068 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                                                              If you use plots from MultiQC in a publication or presentation, please cite:

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                                                              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                              + Bioinformatics (2016)
                                                              + doi: 10.1093/bioinformatics/btw354
                                                              + PMID: 27312411 +
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                                                              Tool Citations

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                                                              Please remember to cite the tools that you use in your analysis.

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                                                              To help with this, you can download publication details of the tools mentioned in this report:

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                                                              About MultiQC

                                                              +

                                                              This report was generated using MultiQC, version 1.12

                                                              +

                                                              You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                                                              +

                                                              For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                              +

                                                              You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                              +

                                                              MultiQC is published in Bioinformatics:

                                                              +
                                                              + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                              + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                              + Bioinformatics (2016)
                                                              + doi: 10.1093/bioinformatics/btw354
                                                              + PMID: 27312411 +
                                                              +
                                                              + +
                                                              + +
                                                              + + +
                                                              + + + +

                                                              + + + + +

                                                              + + + +

                                                              + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                              + + + + + + + + + + + +
                                                              +

                                                              Report + + generated on 2022-02-15, 02:32 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/CWNC/logs/b5/18c58258978a13945eda7b1782f5b0

                                                              + + +
                                                              + + + + + + + +
                                                              + + + + + + + + +
                                                              +

                                                              General Statistics

                                                              + + + + + + + + + + + Showing 34/34 rows and 2/2 columns. + +
                                                              +
                                                              + +
                                                              Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                              10_150304_L001.assemble_contigs
                                                              1.2Kbp
                                                              1904.1Mbp
                                                              12_150304_L004.assemble_contigs
                                                              1.2Kbp
                                                              1945.6Mbp
                                                              13_RB103T_C_150611_L007.assemble_contigs
                                                              1.3Kbp
                                                              2097.9Mbp
                                                              18_RB108T_C_150611_L008.assemble_contigs
                                                              1.1Kbp
                                                              1872.0Mbp
                                                              22_150304_L004.assemble_contigs
                                                              1.2Kbp
                                                              1984.1Mbp
                                                              27_150304_L003.assemble_contigs
                                                              1.1Kbp
                                                              1879.0Mbp
                                                              28_RB118T_C_150616_L003.assemble_contigs
                                                              1.4Kbp
                                                              2010.9Mbp
                                                              30_RB122T_C_150616_L004.assemble_contigs
                                                              1.4Kbp
                                                              2049.0Mbp
                                                              39_150304_L002.assemble_contigs
                                                              1.3Kbp
                                                              1916.0Mbp
                                                              CB12.assemble_contigs
                                                              6.7Kbp
                                                              2693.0Mbp
                                                              CB14.assemble_contigs
                                                              6.4Kbp
                                                              2674.9Mbp
                                                              CB15.assemble_contigs
                                                              6.5Kbp
                                                              2692.6Mbp
                                                              CB16.assemble_contigs
                                                              6.3Kbp
                                                              2689.1Mbp
                                                              CB17.assemble_contigs
                                                              4.9Kbp
                                                              2699.5Mbp
                                                              CB24.assemble_contigs
                                                              6.6Kbp
                                                              2692.1Mbp
                                                              CB29.assemble_contigs
                                                              5.3Kbp
                                                              2698.7Mbp
                                                              CB31.assemble_contigs
                                                              6.5Kbp
                                                              2690.9Mbp
                                                              CB32.assemble_contigs
                                                              5.4Kbp
                                                              2682.4Mbp
                                                              CB33.assemble_contigs
                                                              6.5Kbp
                                                              2676.9Mbp
                                                              CB7.assemble_contigs
                                                              6.3Kbp
                                                              2677.7Mbp
                                                              CF24.assemble_contigs
                                                              6.4Kbp
                                                              2689.1Mbp
                                                              CF25.assemble_contigs
                                                              6.4Kbp
                                                              2689.5Mbp
                                                              CF26.assemble_contigs
                                                              6.2Kbp
                                                              2680.6Mbp
                                                              CF27.assemble_contigs
                                                              6.3Kbp
                                                              2692.9Mbp
                                                              CF30.assemble_contigs
                                                              6.7Kbp
                                                              2691.1Mbp
                                                              CF37.assemble_contigs
                                                              6.5Kbp
                                                              2688.5Mbp
                                                              CF46.assemble_contigs
                                                              6.2Kbp
                                                              2671.4Mbp
                                                              CF49.assemble_contigs
                                                              6.3Kbp
                                                              2673.5Mbp
                                                              CP17.assemble_contigs
                                                              6.0Kbp
                                                              2672.2Mbp
                                                              CP28.assemble_contigs
                                                              6.7Kbp
                                                              2691.5Mbp
                                                              CP36.assemble_contigs
                                                              5.8Kbp
                                                              2679.1Mbp
                                                              CP38.assemble_contigs
                                                              5.9Kbp
                                                              2679.4Mbp
                                                              CP40.assemble_contigs
                                                              5.4Kbp
                                                              2698.9Mbp
                                                              CP48.assemble_contigs
                                                              5.9Kbp
                                                              2679.7Mbp
                                                              + + +
                                                              + + + + + + +
                                                              + + +
                                                              +

                                                              QUAST

                                                              +

                                                              QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                              + + + + +
                                                              + +

                                                              + Assembly Statistics + +

                                                              + + + + +
                                                              + + + + + + + + + Showing 34/34 rows and 10/10 columns. + +
                                                              +
                                                              + +
                                                              Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                              10_150304_L001.assemble_contigs
                                                              1.2Kbp
                                                              0.8Kbp
                                                              509.6K
                                                              1006.2K
                                                              24.2Kbp
                                                              1904.1Mbp
                                                              1511.0
                                                              99.85
                                                              14.72
                                                              61.4%
                                                              12_150304_L004.assemble_contigs
                                                              1.2Kbp
                                                              0.8Kbp
                                                              517.9K
                                                              1023.8K
                                                              14.5Kbp
                                                              1945.6Mbp
                                                              1439.0
                                                              96.38
                                                              14.00
                                                              62.7%
                                                              13_RB103T_C_150611_L007.assemble_contigs
                                                              1.3Kbp
                                                              0.8Kbp
                                                              485.4K
                                                              982.3K
                                                              19.0Kbp
                                                              2097.9Mbp
                                                              1652.0
                                                              99.54
                                                              14.24
                                                              67.4%
                                                              18_RB108T_C_150611_L008.assemble_contigs
                                                              1.1Kbp
                                                              0.8Kbp
                                                              535.4K
                                                              1045.6K
                                                              12.8Kbp
                                                              1872.0Mbp
                                                              1518.0
                                                              95.63
                                                              13.90
                                                              60.4%
                                                              22_150304_L004.assemble_contigs
                                                              1.2Kbp
                                                              0.8Kbp
                                                              500.2K
                                                              997.1K
                                                              15.7Kbp
                                                              1984.1Mbp
                                                              1465.0
                                                              98.21
                                                              14.35
                                                              63.9%
                                                              27_150304_L003.assemble_contigs
                                                              1.1Kbp
                                                              0.8Kbp
                                                              560.6K
                                                              1081.9K
                                                              14.5Kbp
                                                              1879.0Mbp
                                                              1506.0
                                                              95.02
                                                              13.83
                                                              60.7%
                                                              28_RB118T_C_150616_L003.assemble_contigs
                                                              1.4Kbp
                                                              0.9Kbp
                                                              434.6K
                                                              895.1K
                                                              22.1Kbp
                                                              2010.9Mbp
                                                              1559.0
                                                              97.41
                                                              14.07
                                                              64.6%
                                                              30_RB122T_C_150616_L004.assemble_contigs
                                                              1.4Kbp
                                                              0.9Kbp
                                                              419.1K
                                                              876.7K
                                                              23.3Kbp
                                                              2049.0Mbp
                                                              1490.0
                                                              99.56
                                                              14.46
                                                              65.8%
                                                              39_150304_L002.assemble_contigs
                                                              1.3Kbp
                                                              0.8Kbp
                                                              468.8K
                                                              948.5K
                                                              21.3Kbp
                                                              1916.0Mbp
                                                              1350.0
                                                              95.97
                                                              14.24
                                                              61.7%
                                                              CB12.assemble_contigs
                                                              6.7Kbp
                                                              3.5Kbp
                                                              117.4K
                                                              257.0K
                                                              75.6Kbp
                                                              2693.0Mbp
                                                              591.0
                                                              104.75
                                                              20.62
                                                              87.4%
                                                              CB14.assemble_contigs
                                                              6.4Kbp
                                                              3.4Kbp
                                                              121.2K
                                                              264.7K
                                                              64.8Kbp
                                                              2674.9Mbp
                                                              553.0
                                                              104.47
                                                              20.19
                                                              86.8%
                                                              CB15.assemble_contigs
                                                              6.5Kbp
                                                              3.4Kbp
                                                              120.4K
                                                              263.8K
                                                              101.2Kbp
                                                              2692.6Mbp
                                                              628.0
                                                              105.01
                                                              20.66
                                                              87.3%
                                                              CB16.assemble_contigs
                                                              6.3Kbp
                                                              3.3Kbp
                                                              123.2K
                                                              270.4K
                                                              72.7Kbp
                                                              2689.1Mbp
                                                              587.0
                                                              104.23
                                                              20.25
                                                              87.2%
                                                              CB17.assemble_contigs
                                                              4.9Kbp
                                                              2.6Kbp
                                                              162.5K
                                                              351.9K
                                                              71.4Kbp
                                                              2699.5Mbp
                                                              725.0
                                                              105.12
                                                              20.73
                                                              87.0%
                                                              CB24.assemble_contigs
                                                              6.6Kbp
                                                              3.4Kbp
                                                              118.0K
                                                              258.4K
                                                              74.9Kbp
                                                              2692.1Mbp
                                                              693.0
                                                              104.59
                                                              20.33
                                                              87.3%
                                                              CB29.assemble_contigs
                                                              5.3Kbp
                                                              2.8Kbp
                                                              148.4K
                                                              322.1K
                                                              65.4Kbp
                                                              2698.7Mbp
                                                              648.0
                                                              104.36
                                                              20.31
                                                              87.1%
                                                              CB31.assemble_contigs
                                                              6.5Kbp
                                                              3.4Kbp
                                                              119.7K
                                                              262.3K
                                                              77.5Kbp
                                                              2690.9Mbp
                                                              625.0
                                                              104.44
                                                              20.30
                                                              87.3%
                                                              CB32.assemble_contigs
                                                              5.4Kbp
                                                              2.9Kbp
                                                              145.1K
                                                              315.1K
                                                              78.1Kbp
                                                              2682.4Mbp
                                                              686.0
                                                              104.88
                                                              20.46
                                                              86.7%
                                                              CB33.assemble_contigs
                                                              6.5Kbp
                                                              3.4Kbp
                                                              120.9K
                                                              264.3K
                                                              68.5Kbp
                                                              2676.9Mbp
                                                              611.0
                                                              104.70
                                                              20.27
                                                              86.8%
                                                              CB7.assemble_contigs
                                                              6.3Kbp
                                                              3.3Kbp
                                                              123.0K
                                                              268.4K
                                                              76.2Kbp
                                                              2677.7Mbp
                                                              607.0
                                                              104.89
                                                              20.30
                                                              86.8%
                                                              CF24.assemble_contigs
                                                              6.4Kbp
                                                              3.3Kbp
                                                              121.0K
                                                              265.4K
                                                              78.7Kbp
                                                              2689.1Mbp
                                                              613.0
                                                              104.11
                                                              20.29
                                                              87.2%
                                                              CF25.assemble_contigs
                                                              6.4Kbp
                                                              3.3Kbp
                                                              121.6K
                                                              267.2K
                                                              80.5Kbp
                                                              2689.5Mbp
                                                              594.0
                                                              103.85
                                                              20.40
                                                              87.2%
                                                              CF26.assemble_contigs
                                                              6.2Kbp
                                                              3.3Kbp
                                                              125.2K
                                                              273.5K
                                                              68.5Kbp
                                                              2680.6Mbp
                                                              707.0
                                                              104.61
                                                              20.40
                                                              86.9%
                                                              CF27.assemble_contigs
                                                              6.3Kbp
                                                              3.3Kbp
                                                              124.8K
                                                              272.9K
                                                              82.5Kbp
                                                              2692.9Mbp
                                                              679.0
                                                              104.41
                                                              20.39
                                                              87.3%
                                                              CF30.assemble_contigs
                                                              6.7Kbp
                                                              3.5Kbp
                                                              117.2K
                                                              256.6K
                                                              70.5Kbp
                                                              2691.1Mbp
                                                              608.0
                                                              103.95
                                                              20.40
                                                              87.3%
                                                              CF37.assemble_contigs
                                                              6.5Kbp
                                                              3.4Kbp
                                                              119.5K
                                                              262.7K
                                                              76.4Kbp
                                                              2688.5Mbp
                                                              590.0
                                                              103.79
                                                              20.26
                                                              87.2%
                                                              CF46.assemble_contigs
                                                              6.2Kbp
                                                              3.3Kbp
                                                              124.6K
                                                              272.1K
                                                              75.1Kbp
                                                              2671.4Mbp
                                                              675.0
                                                              104.22
                                                              20.06
                                                              86.6%
                                                              CF49.assemble_contigs
                                                              6.3Kbp
                                                              3.3Kbp
                                                              124.5K
                                                              272.3K
                                                              74.3Kbp
                                                              2673.5Mbp
                                                              599.0
                                                              103.89
                                                              20.06
                                                              86.7%
                                                              CP17.assemble_contigs
                                                              6.0Kbp
                                                              3.1Kbp
                                                              129.4K
                                                              283.7K
                                                              67.2Kbp
                                                              2672.2Mbp
                                                              670.0
                                                              103.99
                                                              20.23
                                                              86.6%
                                                              CP28.assemble_contigs
                                                              6.7Kbp
                                                              3.5Kbp
                                                              116.8K
                                                              256.1K
                                                              82.6Kbp
                                                              2691.5Mbp
                                                              601.0
                                                              104.29
                                                              20.40
                                                              87.3%
                                                              CP36.assemble_contigs
                                                              5.8Kbp
                                                              3.1Kbp
                                                              135.2K
                                                              293.8K
                                                              60.7Kbp
                                                              2679.1Mbp
                                                              673.0
                                                              104.08
                                                              20.14
                                                              86.7%
                                                              CP38.assemble_contigs
                                                              5.9Kbp
                                                              3.1Kbp
                                                              132.0K
                                                              287.6K
                                                              82.4Kbp
                                                              2679.4Mbp
                                                              627.0
                                                              104.19
                                                              20.17
                                                              86.8%
                                                              CP40.assemble_contigs
                                                              5.4Kbp
                                                              2.9Kbp
                                                              146.4K
                                                              317.4K
                                                              61.1Kbp
                                                              2698.9Mbp
                                                              707.0
                                                              104.61
                                                              20.50
                                                              87.2%
                                                              CP48.assemble_contigs
                                                              5.9Kbp
                                                              3.1Kbp
                                                              133.2K
                                                              290.2K
                                                              71.0Kbp
                                                              2679.7Mbp
                                                              616.0
                                                              104.68
                                                              20.37
                                                              86.7%
                                                              + +
                                                              + + +
                                                              +
                                                              + + +
                                                              + + + + + +
                                                              + +

                                                              + Number of Contigs + +

                                                              + +

                                                              This plot shows the number of contigs found for each assembly, broken + down by length.

                                                              + + +
                                                              + + +
                                                              +
                                                              loading..
                                                              +
                                                              + + + +
                                                              + + + +
                                                              +
                                                              + + + +
                                                              + + +
                                                              +

                                                              BUSCO

                                                              +

                                                              BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                              + + + + +
                                                              + +

                                                              + Lineage: eukaryota_odb10 + +

                                                              + + + + +
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                                                              loading..
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                                                              + + +
                                                              + + +
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                                                              + +
                                                              +
                                                              + + +

                                                              + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                              +

                                                              + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

                                                              +
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                                                                    +
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                                                                    If you use plots from MultiQC in a publication or presentation, please cite:

                                                                    +
                                                                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                    + Bioinformatics (2016)
                                                                    + doi: 10.1093/bioinformatics/btw354
                                                                    + PMID: 27312411 +
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                                                                    Tool Citations

                                                                    +

                                                                    Please remember to cite the tools that you use in your analysis.

                                                                    +

                                                                    To help with this, you can download publication details of the tools mentioned in this report:

                                                                    +

                                                                    +

                                                                    +
                                                                    + + +
                                                                    +

                                                                    About MultiQC

                                                                    +

                                                                    This report was generated using MultiQC, version 1.12

                                                                    +

                                                                    You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                                                                    +

                                                                    For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                                    +

                                                                    You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                                    +

                                                                    MultiQC is published in Bioinformatics:

                                                                    +
                                                                    + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                    + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                    + Bioinformatics (2016)
                                                                    + doi: 10.1093/bioinformatics/btw354
                                                                    + PMID: 27312411 +
                                                                    +
                                                                    + +
                                                                    + +
                                                                    + + +
                                                                    + + + +

                                                                    + + + + +

                                                                    + + + +

                                                                    + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                                    + + + + + + + + + + + +
                                                                    +

                                                                    Report + + generated on 2022-02-10, 01:48 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/EAAA/logs/cf/1dc031e6d9977611275531e143d0a5

                                                                    + + +
                                                                    + + + + + + + +
                                                                    + + + + + + + + +
                                                                    +

                                                                    General Statistics

                                                                    + + + + + + + + + + + Showing 5/5 rows and 2/2 columns. + +
                                                                    +
                                                                    + +
                                                                    Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                    LP6005442_DNA_D09.assemble_contigs
                                                                    1.1Kbp
                                                                    2101.9Mbp
                                                                    egpg5305762.assemble_contigs
                                                                    1.7Kbp
                                                                    2016.7Mbp
                                                                    egpg5305920.assemble_contigs
                                                                    1.3Kbp
                                                                    2070.7Mbp
                                                                    egpg5305949.assemble_contigs
                                                                    1.3Kbp
                                                                    2036.2Mbp
                                                                    egpg5305974.assemble_contigs
                                                                    1.5Kbp
                                                                    2292.4Mbp
                                                                    + + +
                                                                    + + + + + + +
                                                                    + + +
                                                                    +

                                                                    QUAST

                                                                    +

                                                                    QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                                    + + + + +
                                                                    + +

                                                                    + Assembly Statistics + +

                                                                    + + + + +
                                                                    + + + + + + + + + Showing 5/5 rows and 10/10 columns. + +
                                                                    +
                                                                    + +
                                                                    Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                    LP6005442_DNA_D09.assemble_contigs
                                                                    1.1Kbp
                                                                    0.8Kbp
                                                                    597.4K
                                                                    1169.3K
                                                                    12.6Kbp
                                                                    2101.9Mbp
                                                                    1063.0
                                                                    77.87
                                                                    12.51
                                                                    67.1%
                                                                    egpg5305762.assemble_contigs
                                                                    1.7Kbp
                                                                    1.0Kbp
                                                                    359.1K
                                                                    753.9K
                                                                    30.8Kbp
                                                                    2016.7Mbp
                                                                    1504.0
                                                                    91.17
                                                                    13.97
                                                                    64.8%
                                                                    egpg5305920.assemble_contigs
                                                                    1.3Kbp
                                                                    0.9Kbp
                                                                    473.3K
                                                                    962.7K
                                                                    24.5Kbp
                                                                    2070.7Mbp
                                                                    1454.0
                                                                    86.94
                                                                    12.59
                                                                    66.7%
                                                                    egpg5305949.assemble_contigs
                                                                    1.3Kbp
                                                                    0.8Kbp
                                                                    482.7K
                                                                    975.3K
                                                                    45.4Kbp
                                                                    2036.2Mbp
                                                                    1581.0
                                                                    86.48
                                                                    12.03
                                                                    65.5%
                                                                    egpg5305974.assemble_contigs
                                                                    1.5Kbp
                                                                    0.9Kbp
                                                                    446.3K
                                                                    927.8K
                                                                    30.1Kbp
                                                                    2292.4Mbp
                                                                    1672.0
                                                                    87.41
                                                                    13.45
                                                                    73.6%
                                                                    + +
                                                                    + + +
                                                                    +
                                                                    + + +
                                                                    + + + + + +
                                                                    + +

                                                                    + Number of Contigs + +

                                                                    + +

                                                                    This plot shows the number of contigs found for each assembly, broken + down by length.

                                                                    + + +
                                                                    + + +
                                                                    +
                                                                    loading..
                                                                    +
                                                                    + + + +
                                                                    + + + +
                                                                    +
                                                                    + + + +
                                                                    + + +
                                                                    +

                                                                    BUSCO

                                                                    +

                                                                    BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                    + + + + +
                                                                    + +

                                                                    + Lineage: eukaryota_odb10 + +

                                                                    + + + + +
                                                                    + + +
                                                                    +
                                                                    loading..
                                                                    +
                                                                    + + + +
                                                                    + + +
                                                                    + + +
                                                                    + + + + +
                                                                    + +
                                                                    +
                                                                    + + +

                                                                    + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                                    +

                                                                    + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

                                                                    +
                                                                    +
                                                                    + + + + + + + + + + + + + + diff --git a/dataAnalysis/multiQC/finalDataset/EANS_report.html b/dataAnalysis/multiQC/finalDataset/EANS_report.html new file mode 100644 index 0000000..8f4d570 --- /dev/null +++ b/dataAnalysis/multiQC/finalDataset/EANS_report.html @@ -0,0 +1,6068 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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                                                                          Download the raw data used to create the plots in this report below:

                                                                          +
                                                                          +
                                                                          + +
                                                                          +
                                                                          + +
                                                                          +
                                                                          + +

                                                                          Note that additional data was saved in multiqc_data when this report was generated.

                                                                          + +
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                                                                          + +
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                                                                          Choose Plots
                                                                          + + +
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                                                                          + +

                                                                          If you use plots from MultiQC in a publication or presentation, please cite:

                                                                          +
                                                                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                          + Bioinformatics (2016)
                                                                          + doi: 10.1093/bioinformatics/btw354
                                                                          + PMID: 27312411 +
                                                                          +
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                                                                          +

                                                                          Tool Citations

                                                                          +

                                                                          Please remember to cite the tools that you use in your analysis.

                                                                          +

                                                                          To help with this, you can download publication details of the tools mentioned in this report:

                                                                          +

                                                                          +

                                                                          +
                                                                          + + +
                                                                          +

                                                                          About MultiQC

                                                                          +

                                                                          This report was generated using MultiQC, version 1.12

                                                                          +

                                                                          You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                                                                          +

                                                                          For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                                          +

                                                                          You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                                          +

                                                                          MultiQC is published in Bioinformatics:

                                                                          +
                                                                          + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                          + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                          + Bioinformatics (2016)
                                                                          + doi: 10.1093/bioinformatics/btw354
                                                                          + PMID: 27312411 +
                                                                          +
                                                                          + +
                                                                          + +
                                                                          + + +
                                                                          + + + +

                                                                          + + + + +

                                                                          + + + +

                                                                          + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                                          + + + + + + + + + + + +
                                                                          +

                                                                          Report + + generated on 2022-02-15, 23:51 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/EANS/logs/98/ab813fde59732ba238f4e66791355b

                                                                          + + +
                                                                          + + + + + + + +
                                                                          + + + + + + + + +
                                                                          +

                                                                          General Statistics

                                                                          + + + + + + + + + + + Showing 18/18 rows and 2/2 columns. + +
                                                                          +
                                                                          + +
                                                                          Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                          10_UO_113T_150731_L003.assemble_contigs
                                                                          1.1Kbp
                                                                          1884.2Mbp
                                                                          13_UO_134T_150731_L005.assemble_contigs
                                                                          1.3Kbp
                                                                          2074.9Mbp
                                                                          16_UO_142T_150731_L006.assemble_contigs
                                                                          1.2Kbp
                                                                          1935.3Mbp
                                                                          17_UO_144T_150731_L007.assemble_contigs
                                                                          1.3Kbp
                                                                          1974.7Mbp
                                                                          1_UO_005T_150730_L001.assemble_contigs
                                                                          1.2Kbp
                                                                          1925.3Mbp
                                                                          22_UO_045C_150813_L002.assemble_contigs
                                                                          1.3Kbp
                                                                          1943.6Mbp
                                                                          27_UO_072C_150813_L001.assemble_contigs
                                                                          1.3Kbp
                                                                          1999.4Mbp
                                                                          35_UO_090C_150813_L005.assemble_contigs
                                                                          1.2Kbp
                                                                          1912.0Mbp
                                                                          39_UO_098C_150902_L002.assemble_contigs
                                                                          1.7Kbp
                                                                          2181.8Mbp
                                                                          42_UO_105C_150902_L003.assemble_contigs
                                                                          1.3Kbp
                                                                          2035.2Mbp
                                                                          43_UO_106C_150902_L004.assemble_contigs
                                                                          1.1Kbp
                                                                          1878.4Mbp
                                                                          44_UO_107C_150902_L004.assemble_contigs
                                                                          1.1Kbp
                                                                          1873.6Mbp
                                                                          47_UO_115C_150902_L006.assemble_contigs
                                                                          1.2Kbp
                                                                          1989.4Mbp
                                                                          6_UO_069T_150731_L001.assemble_contigs
                                                                          1.3Kbp
                                                                          2055.9Mbp
                                                                          7_UO_071T_150731_L002.assemble_contigs
                                                                          1.2Kbp
                                                                          1914.9Mbp
                                                                          8_UO_074T_150731_L002.assemble_contigs
                                                                          1.1Kbp
                                                                          1864.2Mbp
                                                                          LP6005443_DNA_F06.assemble_contigs
                                                                          1.3Kbp
                                                                          2166.7Mbp
                                                                          egpg5305814.assemble_contigs
                                                                          1.2Kbp
                                                                          2039.1Mbp
                                                                          + + +
                                                                          + + + + + + +
                                                                          + + +
                                                                          +

                                                                          QUAST

                                                                          +

                                                                          QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                                          + + + + +
                                                                          + +

                                                                          + Assembly Statistics + +

                                                                          + + + + +
                                                                          + + + + + + + + + Showing 18/18 rows and 10/10 columns. + +
                                                                          +
                                                                          + +
                                                                          Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                          10_UO_113T_150731_L003.assemble_contigs
                                                                          1.1Kbp
                                                                          0.8Kbp
                                                                          546.5K
                                                                          1056.7K
                                                                          13.2Kbp
                                                                          1884.2Mbp
                                                                          1499.0
                                                                          95.00
                                                                          13.57
                                                                          60.8%
                                                                          13_UO_134T_150731_L005.assemble_contigs
                                                                          1.3Kbp
                                                                          0.9Kbp
                                                                          478.2K
                                                                          965.2K
                                                                          21.8Kbp
                                                                          2074.9Mbp
                                                                          1535.0
                                                                          98.67
                                                                          14.19
                                                                          66.7%
                                                                          16_UO_142T_150731_L006.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          538.8K
                                                                          1048.9K
                                                                          13.5Kbp
                                                                          1935.3Mbp
                                                                          1530.0
                                                                          95.58
                                                                          13.67
                                                                          62.4%
                                                                          17_UO_144T_150731_L007.assemble_contigs
                                                                          1.3Kbp
                                                                          0.8Kbp
                                                                          491.4K
                                                                          979.2K
                                                                          15.4Kbp
                                                                          1974.7Mbp
                                                                          1467.0
                                                                          98.24
                                                                          14.18
                                                                          63.6%
                                                                          1_UO_005T_150730_L001.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          497.1K
                                                                          984.2K
                                                                          12.8Kbp
                                                                          1925.3Mbp
                                                                          1691.0
                                                                          97.60
                                                                          14.00
                                                                          62.0%
                                                                          22_UO_045C_150813_L002.assemble_contigs
                                                                          1.3Kbp
                                                                          0.8Kbp
                                                                          478.2K
                                                                          957.3K
                                                                          15.8Kbp
                                                                          1943.6Mbp
                                                                          1492.0
                                                                          98.15
                                                                          14.30
                                                                          62.5%
                                                                          27_UO_072C_150813_L001.assemble_contigs
                                                                          1.3Kbp
                                                                          0.8Kbp
                                                                          501.3K
                                                                          994.5K
                                                                          23.5Kbp
                                                                          1999.4Mbp
                                                                          1492.0
                                                                          98.14
                                                                          14.28
                                                                          64.4%
                                                                          35_UO_090C_150813_L005.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          510.7K
                                                                          1002.9K
                                                                          13.6Kbp
                                                                          1912.0Mbp
                                                                          1594.0
                                                                          97.62
                                                                          13.92
                                                                          61.6%
                                                                          39_UO_098C_150902_L002.assemble_contigs
                                                                          1.7Kbp
                                                                          1.0Kbp
                                                                          376.8K
                                                                          805.0K
                                                                          24.9Kbp
                                                                          2181.8Mbp
                                                                          1624.0
                                                                          101.32
                                                                          14.28
                                                                          70.1%
                                                                          42_UO_105C_150902_L003.assemble_contigs
                                                                          1.3Kbp
                                                                          0.8Kbp
                                                                          508.3K
                                                                          1007.9K
                                                                          21.7Kbp
                                                                          2035.2Mbp
                                                                          1542.0
                                                                          98.82
                                                                          14.17
                                                                          65.5%
                                                                          43_UO_106C_150902_L004.assemble_contigs
                                                                          1.1Kbp
                                                                          0.8Kbp
                                                                          533.7K
                                                                          1035.1K
                                                                          13.2Kbp
                                                                          1878.4Mbp
                                                                          1433.0
                                                                          97.64
                                                                          13.87
                                                                          60.6%
                                                                          44_UO_107C_150902_L004.assemble_contigs
                                                                          1.1Kbp
                                                                          0.8Kbp
                                                                          535.9K
                                                                          1038.0K
                                                                          13.2Kbp
                                                                          1873.6Mbp
                                                                          1552.0
                                                                          97.02
                                                                          13.66
                                                                          60.4%
                                                                          47_UO_115C_150902_L006.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          532.8K
                                                                          1041.7K
                                                                          14.4Kbp
                                                                          1989.4Mbp
                                                                          1536.0
                                                                          96.12
                                                                          13.63
                                                                          64.1%
                                                                          6_UO_069T_150731_L001.assemble_contigs
                                                                          1.3Kbp
                                                                          0.9Kbp
                                                                          468.4K
                                                                          949.5K
                                                                          18.4Kbp
                                                                          2055.9Mbp
                                                                          1501.0
                                                                          98.67
                                                                          14.34
                                                                          66.1%
                                                                          7_UO_071T_150731_L002.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          516.7K
                                                                          1012.1K
                                                                          13.6Kbp
                                                                          1914.9Mbp
                                                                          1413.0
                                                                          97.86
                                                                          13.75
                                                                          61.7%
                                                                          8_UO_074T_150731_L002.assemble_contigs
                                                                          1.1Kbp
                                                                          0.8Kbp
                                                                          519.1K
                                                                          1015.1K
                                                                          13.8Kbp
                                                                          1864.2Mbp
                                                                          1471.0
                                                                          95.18
                                                                          13.45
                                                                          60.1%
                                                                          LP6005443_DNA_F06.assemble_contigs
                                                                          1.3Kbp
                                                                          0.8Kbp
                                                                          512.7K
                                                                          1044.5K
                                                                          18.4Kbp
                                                                          2166.7Mbp
                                                                          1208.0
                                                                          82.48
                                                                          13.39
                                                                          69.2%
                                                                          egpg5305814.assemble_contigs
                                                                          1.2Kbp
                                                                          0.8Kbp
                                                                          509.6K
                                                                          1020.5K
                                                                          43.5Kbp
                                                                          2039.1Mbp
                                                                          1556.0
                                                                          91.98
                                                                          12.77
                                                                          65.6%
                                                                          + +
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                                                                          + + + + + +
                                                                          + +

                                                                          + Number of Contigs + +

                                                                          + +

                                                                          This plot shows the number of contigs found for each assembly, broken + down by length.

                                                                          + + +
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                                                                          loading..
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                                                                          +

                                                                          BUSCO

                                                                          +

                                                                          BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                          + + + + +
                                                                          + +

                                                                          + Lineage: eukaryota_odb10 + +

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                                                                          + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

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                                                                          + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

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                                                                                + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                + Bioinformatics (2016)
                                                                                + doi: 10.1093/bioinformatics/btw354
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                                                                                Tool Citations

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                                                                                Please remember to cite the tools that you use in your analysis.

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                                                                                About MultiQC

                                                                                +

                                                                                This report was generated using MultiQC, version 1.12

                                                                                +

                                                                                You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

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                                                                                For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                                                +

                                                                                You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                                                +

                                                                                MultiQC is published in Bioinformatics:

                                                                                +
                                                                                + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                + Bioinformatics (2016)
                                                                                + doi: 10.1093/bioinformatics/btw354
                                                                                + PMID: 27312411 +
                                                                                +
                                                                                + +
                                                                                + +
                                                                                + + +
                                                                                + + + +

                                                                                + + + + +

                                                                                + + + +

                                                                                + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                                                + + + + + + + + + + + +
                                                                                +

                                                                                Report + + generated on 2022-02-16, 01:40 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/FWNC/logs/85/dac2781488b5e179cb0386bdd8e0fa

                                                                                + + +
                                                                                + + + + + + + +
                                                                                + + + + + + + + +
                                                                                +

                                                                                General Statistics

                                                                                + + + + + + + + + + + Showing 35/35 rows and 2/2 columns. + +
                                                                                +
                                                                                + +
                                                                                Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                HG03225.assemble_contigs
                                                                                8.3Kbp
                                                                                2722.4Mbp
                                                                                HG03380.assemble_contigs
                                                                                8.1Kbp
                                                                                2705.7Mbp
                                                                                HG03385.assemble_contigs
                                                                                9.7Kbp
                                                                                2749.9Mbp
                                                                                HG03388.assemble_contigs
                                                                                8.3Kbp
                                                                                2720.8Mbp
                                                                                HG03449.assemble_contigs
                                                                                8.1Kbp
                                                                                2705.0Mbp
                                                                                IAJ0K.assemble_contigs
                                                                                6.4Kbp
                                                                                2673.4Mbp
                                                                                IAM0N.assemble_contigs
                                                                                6.4Kbp
                                                                                2674.2Mbp
                                                                                IAP0Q.assemble_contigs
                                                                                6.5Kbp
                                                                                2694.4Mbp
                                                                                IBJ0M.assemble_contigs
                                                                                6.3Kbp
                                                                                2673.2Mbp
                                                                                IBQ0T.assemble_contigs
                                                                                6.4Kbp
                                                                                2675.8Mbp
                                                                                LP6005441_DNA_F07.assemble_contigs
                                                                                1.0Kbp
                                                                                1948.4Mbp
                                                                                LZP0B.assemble_contigs
                                                                                6.8Kbp
                                                                                2691.8Mbp
                                                                                NA18498.assemble_contigs
                                                                                7.8Kbp
                                                                                2725.2Mbp
                                                                                NA18499.assemble_contigs
                                                                                10.2Kbp
                                                                                2735.3Mbp
                                                                                NA18501.assemble_contigs
                                                                                7.5Kbp
                                                                                2726.0Mbp
                                                                                NA18504.assemble_contigs
                                                                                8.0Kbp
                                                                                2722.1Mbp
                                                                                NA18505.assemble_contigs
                                                                                8.1Kbp
                                                                                2701.5Mbp
                                                                                NA19099.assemble_contigs
                                                                                8.5Kbp
                                                                                2703.3Mbp
                                                                                NA19107.assemble_contigs
                                                                                9.3Kbp
                                                                                2750.0Mbp
                                                                                NA19118.assemble_contigs
                                                                                8.4Kbp
                                                                                2703.0Mbp
                                                                                NA19129.assemble_contigs
                                                                                10.8Kbp
                                                                                2734.4Mbp
                                                                                NA19131.assemble_contigs
                                                                                12.0Kbp
                                                                                2732.8Mbp
                                                                                PAV0Q.assemble_contigs
                                                                                6.7Kbp
                                                                                2693.0Mbp
                                                                                PAZ0V.assemble_contigs
                                                                                6.7Kbp
                                                                                2677.5Mbp
                                                                                PBA0X.assemble_contigs
                                                                                6.8Kbp
                                                                                2692.6Mbp
                                                                                PBC0A.assemble_contigs
                                                                                6.7Kbp
                                                                                2677.5Mbp
                                                                                SAMEA2580885.assemble_contigs
                                                                                4.9Kbp
                                                                                2720.3Mbp
                                                                                SAMEA2580886.assemble_contigs
                                                                                5.8Kbp
                                                                                2719.7Mbp
                                                                                SAMEA2580889.assemble_contigs
                                                                                5.8Kbp
                                                                                2714.4Mbp
                                                                                SAMEA2580891.assemble_contigs
                                                                                5.9Kbp
                                                                                2699.9Mbp
                                                                                SAMEA2580897.assemble_contigs
                                                                                7.9Kbp
                                                                                2726.5Mbp
                                                                                SAMEA3506075.assemble_contigs
                                                                                10.1Kbp
                                                                                2739.4Mbp
                                                                                SAMEA3506076.assemble_contigs
                                                                                10.8Kbp
                                                                                2722.1Mbp
                                                                                SAMEA3506077.assemble_contigs
                                                                                9.2Kbp
                                                                                2740.3Mbp
                                                                                SAMEA3506078.assemble_contigs
                                                                                7.6Kbp
                                                                                2741.2Mbp
                                                                                + + +
                                                                                + + + + + + +
                                                                                + + +
                                                                                +

                                                                                QUAST

                                                                                +

                                                                                QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                                                + + + + +
                                                                                + +

                                                                                + Assembly Statistics + +

                                                                                + + + + +
                                                                                + + + + + + + + + Showing 35/35 rows and 10/10 columns. + +
                                                                                +
                                                                                + +
                                                                                Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                HG03225.assemble_contigs
                                                                                8.3Kbp
                                                                                4.3Kbp
                                                                                94.3K
                                                                                207.7K
                                                                                120.4Kbp
                                                                                2722.4Mbp
                                                                                1692.0
                                                                                109.29
                                                                                21.41
                                                                                88.4%
                                                                                HG03380.assemble_contigs
                                                                                8.1Kbp
                                                                                4.2Kbp
                                                                                96.4K
                                                                                211.8K
                                                                                137.0Kbp
                                                                                2705.7Mbp
                                                                                1587.0
                                                                                109.02
                                                                                21.21
                                                                                87.8%
                                                                                HG03385.assemble_contigs
                                                                                9.7Kbp
                                                                                5.0Kbp
                                                                                82.1K
                                                                                180.5K
                                                                                175.1Kbp
                                                                                2749.9Mbp
                                                                                1838.0
                                                                                111.24
                                                                                24.88
                                                                                89.1%
                                                                                HG03388.assemble_contigs
                                                                                8.3Kbp
                                                                                4.3Kbp
                                                                                94.1K
                                                                                207.5K
                                                                                196.0Kbp
                                                                                2720.8Mbp
                                                                                1697.0
                                                                                109.32
                                                                                21.38
                                                                                88.3%
                                                                                HG03449.assemble_contigs
                                                                                8.1Kbp
                                                                                4.2Kbp
                                                                                96.2K
                                                                                211.4K
                                                                                129.9Kbp
                                                                                2705.0Mbp
                                                                                1573.0
                                                                                109.28
                                                                                21.15
                                                                                87.8%
                                                                                IAJ0K.assemble_contigs
                                                                                6.4Kbp
                                                                                3.3Kbp
                                                                                121.8K
                                                                                266.5K
                                                                                69.7Kbp
                                                                                2673.4Mbp
                                                                                625.0
                                                                                103.44
                                                                                20.09
                                                                                86.7%
                                                                                IAM0N.assemble_contigs
                                                                                6.4Kbp
                                                                                3.3Kbp
                                                                                121.9K
                                                                                266.6K
                                                                                82.8Kbp
                                                                                2674.2Mbp
                                                                                618.0
                                                                                103.26
                                                                                20.09
                                                                                86.7%
                                                                                IAP0Q.assemble_contigs
                                                                                6.5Kbp
                                                                                3.4Kbp
                                                                                119.9K
                                                                                263.0K
                                                                                81.8Kbp
                                                                                2694.4Mbp
                                                                                684.0
                                                                                103.48
                                                                                20.44
                                                                                87.4%
                                                                                IBJ0M.assemble_contigs
                                                                                6.3Kbp
                                                                                3.3Kbp
                                                                                123.3K
                                                                                269.5K
                                                                                73.1Kbp
                                                                                2673.2Mbp
                                                                                626.0
                                                                                103.39
                                                                                20.08
                                                                                86.7%
                                                                                IBQ0T.assemble_contigs
                                                                                6.4Kbp
                                                                                3.3Kbp
                                                                                121.5K
                                                                                266.1K
                                                                                73.7Kbp
                                                                                2675.8Mbp
                                                                                586.0
                                                                                103.15
                                                                                20.18
                                                                                86.8%
                                                                                LP6005441_DNA_F07.assemble_contigs
                                                                                1.0Kbp
                                                                                0.7Kbp
                                                                                665.2K
                                                                                1255.2K
                                                                                13.4Kbp
                                                                                1948.4Mbp
                                                                                1017.0
                                                                                78.10
                                                                                12.64
                                                                                62.2%
                                                                                LZP0B.assemble_contigs
                                                                                6.8Kbp
                                                                                3.5Kbp
                                                                                114.7K
                                                                                251.7K
                                                                                77.6Kbp
                                                                                2691.8Mbp
                                                                                607.0
                                                                                103.48
                                                                                20.42
                                                                                87.4%
                                                                                NA18498.assemble_contigs
                                                                                7.8Kbp
                                                                                4.1Kbp
                                                                                100.6K
                                                                                220.7K
                                                                                114.7Kbp
                                                                                2725.2Mbp
                                                                                1642.0
                                                                                108.34
                                                                                21.29
                                                                                88.4%
                                                                                NA18499.assemble_contigs
                                                                                10.2Kbp
                                                                                5.3Kbp
                                                                                77.9K
                                                                                171.0K
                                                                                167.8Kbp
                                                                                2735.3Mbp
                                                                                1895.0
                                                                                111.11
                                                                                24.87
                                                                                88.6%
                                                                                NA18501.assemble_contigs
                                                                                7.5Kbp
                                                                                3.9Kbp
                                                                                105.1K
                                                                                231.4K
                                                                                101.2Kbp
                                                                                2726.0Mbp
                                                                                1719.0
                                                                                108.86
                                                                                21.32
                                                                                88.3%
                                                                                NA18504.assemble_contigs
                                                                                8.0Kbp
                                                                                4.1Kbp
                                                                                98.2K
                                                                                216.4K
                                                                                118.3Kbp
                                                                                2722.1Mbp
                                                                                1463.0
                                                                                107.57
                                                                                21.28
                                                                                88.3%
                                                                                NA18505.assemble_contigs
                                                                                8.1Kbp
                                                                                4.2Kbp
                                                                                97.1K
                                                                                213.5K
                                                                                93.3Kbp
                                                                                2701.5Mbp
                                                                                1510.0
                                                                                108.11
                                                                                20.98
                                                                                87.7%
                                                                                NA19099.assemble_contigs
                                                                                8.5Kbp
                                                                                4.4Kbp
                                                                                92.2K
                                                                                202.4K
                                                                                101.8Kbp
                                                                                2703.3Mbp
                                                                                1579.0
                                                                                107.98
                                                                                20.99
                                                                                87.8%
                                                                                NA19107.assemble_contigs
                                                                                9.3Kbp
                                                                                4.8Kbp
                                                                                85.6K
                                                                                188.7K
                                                                                111.4Kbp
                                                                                2750.0Mbp
                                                                                1799.0
                                                                                110.58
                                                                                24.62
                                                                                89.0%
                                                                                NA19118.assemble_contigs
                                                                                8.4Kbp
                                                                                4.3Kbp
                                                                                93.3K
                                                                                204.9K
                                                                                127.5Kbp
                                                                                2703.0Mbp
                                                                                1549.0
                                                                                107.68
                                                                                20.82
                                                                                87.8%
                                                                                NA19129.assemble_contigs
                                                                                10.8Kbp
                                                                                5.6Kbp
                                                                                73.9K
                                                                                161.6K
                                                                                123.6Kbp
                                                                                2734.4Mbp
                                                                                1892.0
                                                                                111.13
                                                                                24.89
                                                                                88.7%
                                                                                NA19131.assemble_contigs
                                                                                12.0Kbp
                                                                                6.2Kbp
                                                                                66.2K
                                                                                145.3K
                                                                                133.7Kbp
                                                                                2732.8Mbp
                                                                                1801.0
                                                                                111.39
                                                                                25.10
                                                                                88.7%
                                                                                PAV0Q.assemble_contigs
                                                                                6.7Kbp
                                                                                3.5Kbp
                                                                                116.2K
                                                                                254.5K
                                                                                86.9Kbp
                                                                                2693.0Mbp
                                                                                648.0
                                                                                103.54
                                                                                20.49
                                                                                87.4%
                                                                                PAZ0V.assemble_contigs
                                                                                6.7Kbp
                                                                                3.5Kbp
                                                                                117.5K
                                                                                256.3K
                                                                                102.2Kbp
                                                                                2677.5Mbp
                                                                                592.0
                                                                                103.41
                                                                                20.20
                                                                                86.9%
                                                                                PBA0X.assemble_contigs
                                                                                6.8Kbp
                                                                                3.5Kbp
                                                                                114.6K
                                                                                251.1K
                                                                                82.7Kbp
                                                                                2692.6Mbp
                                                                                635.0
                                                                                103.68
                                                                                20.49
                                                                                87.4%
                                                                                PBC0A.assemble_contigs
                                                                                6.7Kbp
                                                                                3.5Kbp
                                                                                116.9K
                                                                                255.1K
                                                                                80.9Kbp
                                                                                2677.5Mbp
                                                                                572.0
                                                                                103.63
                                                                                20.27
                                                                                86.9%
                                                                                SAMEA2580885.assemble_contigs
                                                                                4.9Kbp
                                                                                2.5Kbp
                                                                                161.9K
                                                                                355.2K
                                                                                63.0Kbp
                                                                                2720.3Mbp
                                                                                1826.0
                                                                                108.65
                                                                                20.14
                                                                                87.7%
                                                                                SAMEA2580886.assemble_contigs
                                                                                5.8Kbp
                                                                                3.0Kbp
                                                                                135.7K
                                                                                296.9K
                                                                                83.8Kbp
                                                                                2719.7Mbp
                                                                                1736.0
                                                                                108.34
                                                                                20.19
                                                                                88.0%
                                                                                SAMEA2580889.assemble_contigs
                                                                                5.8Kbp
                                                                                3.0Kbp
                                                                                135.4K
                                                                                295.7K
                                                                                87.6Kbp
                                                                                2714.4Mbp
                                                                                1714.0
                                                                                107.94
                                                                                19.88
                                                                                87.9%
                                                                                SAMEA2580891.assemble_contigs
                                                                                5.9Kbp
                                                                                3.1Kbp
                                                                                133.3K
                                                                                290.9K
                                                                                74.3Kbp
                                                                                2699.9Mbp
                                                                                1598.0
                                                                                108.18
                                                                                19.95
                                                                                87.4%
                                                                                SAMEA2580897.assemble_contigs
                                                                                7.9Kbp
                                                                                4.0Kbp
                                                                                98.5K
                                                                                218.4K
                                                                                109.4Kbp
                                                                                2726.5Mbp
                                                                                1412.0
                                                                                107.25
                                                                                24.01
                                                                                88.1%
                                                                                SAMEA3506075.assemble_contigs
                                                                                10.1Kbp
                                                                                5.2Kbp
                                                                                78.2K
                                                                                172.3K
                                                                                122.5Kbp
                                                                                2739.4Mbp
                                                                                1470.0
                                                                                108.36
                                                                                24.30
                                                                                88.8%
                                                                                SAMEA3506076.assemble_contigs
                                                                                10.8Kbp
                                                                                5.5Kbp
                                                                                72.7K
                                                                                160.5K
                                                                                130.5Kbp
                                                                                2722.1Mbp
                                                                                1406.0
                                                                                108.36
                                                                                24.36
                                                                                88.3%
                                                                                SAMEA3506077.assemble_contigs
                                                                                9.2Kbp
                                                                                4.7Kbp
                                                                                86.3K
                                                                                190.2K
                                                                                108.3Kbp
                                                                                2740.3Mbp
                                                                                1478.0
                                                                                108.28
                                                                                24.19
                                                                                88.8%
                                                                                SAMEA3506078.assemble_contigs
                                                                                7.6Kbp
                                                                                3.9Kbp
                                                                                102.9K
                                                                                229.4K
                                                                                111.6Kbp
                                                                                2741.2Mbp
                                                                                1423.0
                                                                                107.91
                                                                                23.84
                                                                                88.6%
                                                                                + +
                                                                                + + +
                                                                                +
                                                                                + + +
                                                                                + + + + + +
                                                                                + +

                                                                                + Number of Contigs + +

                                                                                + +

                                                                                This plot shows the number of contigs found for each assembly, broken + down by length.

                                                                                + + +
                                                                                + + +
                                                                                +
                                                                                loading..
                                                                                +
                                                                                + + + +
                                                                                + + + +
                                                                                +
                                                                                + + + +
                                                                                + + +
                                                                                +

                                                                                BUSCO

                                                                                +

                                                                                BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                                + + + + +
                                                                                + +

                                                                                + Lineage: eukaryota_odb10 + +

                                                                                + + + + +
                                                                                + + +
                                                                                +
                                                                                loading..
                                                                                +
                                                                                + + + +
                                                                                + + +
                                                                                + + +
                                                                                + + + + +
                                                                                + +
                                                                                +
                                                                                + + +

                                                                                + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                                                +

                                                                                + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

                                                                                +
                                                                                +
                                                                                + + + + + + + + + + + + + + diff --git a/dataAnalysis/multiQC/finalDataset/KS_report.html b/dataAnalysis/multiQC/finalDataset/KS_report.html new file mode 100644 index 0000000..f475892 --- /dev/null +++ b/dataAnalysis/multiQC/finalDataset/KS_report.html @@ -0,0 +1,6068 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                                                                                +
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                                                                                      Note that additional data was saved in multiqc_data when this report was generated.

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                                                                                      If you use plots from MultiQC in a publication or presentation, please cite:

                                                                                      +
                                                                                      + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                      + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                      + Bioinformatics (2016)
                                                                                      + doi: 10.1093/bioinformatics/btw354
                                                                                      + PMID: 27312411 +
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                                                                                      Tool Citations

                                                                                      +

                                                                                      Please remember to cite the tools that you use in your analysis.

                                                                                      +

                                                                                      To help with this, you can download publication details of the tools mentioned in this report:

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                                                                                      About MultiQC

                                                                                      +

                                                                                      This report was generated using MultiQC, version 1.12

                                                                                      +

                                                                                      You can see a YouTube video describing how to use MultiQC reports here: + https://youtu.be/qPbIlO_KWN0

                                                                                      +

                                                                                      For more information about MultiQC, including other videos and + extensive documentation, please visit http://multiqc.info

                                                                                      +

                                                                                      You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: + https://github.com/ewels/MultiQC

                                                                                      +

                                                                                      MultiQC is published in Bioinformatics:

                                                                                      +
                                                                                      + MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                      + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                      + Bioinformatics (2016)
                                                                                      + doi: 10.1093/bioinformatics/btw354
                                                                                      + PMID: 27312411 +
                                                                                      +
                                                                                      + +
                                                                                      + +
                                                                                      + + +
                                                                                      + + + +

                                                                                      + + + + +

                                                                                      + + + +

                                                                                      + A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. +

                                                                                      + + + + + + + + + + + +
                                                                                      +

                                                                                      Report + + generated on 2022-02-15, 22:07 + + + based on data in: + + /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/KhoeSan/logs/0a/72750879f1c2d26a267c2a2a456bc7

                                                                                      + + +
                                                                                      + + + + + + + +
                                                                                      + + + + + + + + +
                                                                                      +

                                                                                      General Statistics

                                                                                      + + + + + + + + + + + Showing 19/19 rows and 2/2 columns. + +
                                                                                      +
                                                                                      + +
                                                                                      Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                      KSP062.assemble_contigs
                                                                                      2.2Kbp
                                                                                      2492.7Mbp
                                                                                      KSP065.assemble_contigs
                                                                                      2.2Kbp
                                                                                      2506.1Mbp
                                                                                      KSP069.assemble_contigs
                                                                                      2.3Kbp
                                                                                      2503.4Mbp
                                                                                      KSP092.assemble_contigs
                                                                                      2.3Kbp
                                                                                      2517.1Mbp
                                                                                      KSP096.assemble_contigs
                                                                                      1.7Kbp
                                                                                      2445.2Mbp
                                                                                      KSP103.assemble_contigs
                                                                                      1.8Kbp
                                                                                      2383.6Mbp
                                                                                      KSP106.assemble_contigs
                                                                                      2.1Kbp
                                                                                      2456.8Mbp
                                                                                      KSP116.assemble_contigs
                                                                                      2.5Kbp
                                                                                      2530.2Mbp
                                                                                      KSP134.assemble_contigs
                                                                                      2.2Kbp
                                                                                      2508.1Mbp
                                                                                      KSP137.assemble_contigs
                                                                                      2.0Kbp
                                                                                      2477.1Mbp
                                                                                      KSP139.assemble_contigs
                                                                                      2.6Kbp
                                                                                      2549.4Mbp
                                                                                      KSP140.assemble_contigs
                                                                                      2.4Kbp
                                                                                      2525.9Mbp
                                                                                      KSP146.assemble_contigs
                                                                                      2.5Kbp
                                                                                      2528.9Mbp
                                                                                      KSP152.assemble_contigs
                                                                                      2.2Kbp
                                                                                      2528.4Mbp
                                                                                      KSP155.assemble_contigs
                                                                                      2.3Kbp
                                                                                      2530.8Mbp
                                                                                      KSP224.assemble_contigs
                                                                                      2.4Kbp
                                                                                      2554.3Mbp
                                                                                      KSP228.assemble_contigs
                                                                                      2.3Kbp
                                                                                      2534.6Mbp
                                                                                      LP6005443_DNA_G08.assemble_contigs
                                                                                      1.2Kbp
                                                                                      2150.8Mbp
                                                                                      SAMEA2580840.assemble_contigs
                                                                                      5.2Kbp
                                                                                      2698.9Mbp
                                                                                      + + +
                                                                                      + + + + + + +
                                                                                      + + +
                                                                                      +

                                                                                      QUAST

                                                                                      +

                                                                                      QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                                                      + + + + +
                                                                                      + +

                                                                                      + Assembly Statistics + +

                                                                                      + + + + +
                                                                                      + + + + + + + + + Showing 19/19 rows and 10/10 columns. + +
                                                                                      +
                                                                                      + +
                                                                                      Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                      KSP062.assemble_contigs
                                                                                      2.2Kbp
                                                                                      1.2Kbp
                                                                                      320.5K
                                                                                      705.8K
                                                                                      39.5Kbp
                                                                                      2492.7Mbp
                                                                                      2376.0
                                                                                      108.32
                                                                                      17.11
                                                                                      79.9%
                                                                                      KSP065.assemble_contigs
                                                                                      2.2Kbp
                                                                                      1.2Kbp
                                                                                      316.2K
                                                                                      693.3K
                                                                                      46.7Kbp
                                                                                      2506.1Mbp
                                                                                      2587.0
                                                                                      106.93
                                                                                      17.04
                                                                                      80.3%
                                                                                      KSP069.assemble_contigs
                                                                                      2.3Kbp
                                                                                      1.2Kbp
                                                                                      309.7K
                                                                                      687.7K
                                                                                      42.5Kbp
                                                                                      2503.4Mbp
                                                                                      2061.0
                                                                                      108.16
                                                                                      17.27
                                                                                      80.3%
                                                                                      KSP092.assemble_contigs
                                                                                      2.3Kbp
                                                                                      1.2Kbp
                                                                                      316.3K
                                                                                      692.2K
                                                                                      39.0Kbp
                                                                                      2517.1Mbp
                                                                                      2560.0
                                                                                      107.87
                                                                                      17.37
                                                                                      80.7%
                                                                                      KSP096.assemble_contigs
                                                                                      1.7Kbp
                                                                                      1.0Kbp
                                                                                      419.9K
                                                                                      884.4K
                                                                                      26.8Kbp
                                                                                      2445.2Mbp
                                                                                      7358.0
                                                                                      106.03
                                                                                      17.17
                                                                                      78.0%
                                                                                      KSP103.assemble_contigs
                                                                                      1.8Kbp
                                                                                      1.1Kbp
                                                                                      383.6K
                                                                                      817.4K
                                                                                      25.9Kbp
                                                                                      2383.6Mbp
                                                                                      6297.0
                                                                                      108.18
                                                                                      17.43
                                                                                      76.1%
                                                                                      KSP106.assemble_contigs
                                                                                      2.1Kbp
                                                                                      1.2Kbp
                                                                                      335.5K
                                                                                      731.4K
                                                                                      32.0Kbp
                                                                                      2456.8Mbp
                                                                                      3772.0
                                                                                      109.42
                                                                                      17.17
                                                                                      78.7%
                                                                                      KSP116.assemble_contigs
                                                                                      2.5Kbp
                                                                                      1.3Kbp
                                                                                      279.9K
                                                                                      628.8K
                                                                                      59.0Kbp
                                                                                      2530.2Mbp
                                                                                      2030.0
                                                                                      110.40
                                                                                      17.36
                                                                                      81.3%
                                                                                      KSP134.assemble_contigs
                                                                                      2.2Kbp
                                                                                      1.2Kbp
                                                                                      318.1K
                                                                                      697.2K
                                                                                      40.7Kbp
                                                                                      2508.1Mbp
                                                                                      2803.0
                                                                                      105.88
                                                                                      16.68
                                                                                      80.4%
                                                                                      KSP137.assemble_contigs
                                                                                      2.0Kbp
                                                                                      1.1Kbp
                                                                                      351.4K
                                                                                      762.3K
                                                                                      41.3Kbp
                                                                                      2477.1Mbp
                                                                                      3703.0
                                                                                      104.93
                                                                                      16.79
                                                                                      79.3%
                                                                                      KSP139.assemble_contigs
                                                                                      2.6Kbp
                                                                                      1.4Kbp
                                                                                      270.6K
                                                                                      609.0K
                                                                                      49.9Kbp
                                                                                      2549.4Mbp
                                                                                      1908.0
                                                                                      107.40
                                                                                      17.14
                                                                                      82.0%
                                                                                      KSP140.assemble_contigs
                                                                                      2.4Kbp
                                                                                      1.3Kbp
                                                                                      290.7K
                                                                                      649.1K
                                                                                      44.7Kbp
                                                                                      2525.9Mbp
                                                                                      2058.0
                                                                                      106.49
                                                                                      16.81
                                                                                      81.1%
                                                                                      KSP146.assemble_contigs
                                                                                      2.5Kbp
                                                                                      1.3Kbp
                                                                                      283.6K
                                                                                      634.6K
                                                                                      48.4Kbp
                                                                                      2528.9Mbp
                                                                                      1879.0
                                                                                      107.57
                                                                                      16.96
                                                                                      81.3%
                                                                                      KSP152.assemble_contigs
                                                                                      2.2Kbp
                                                                                      1.2Kbp
                                                                                      324.0K
                                                                                      710.1K
                                                                                      38.7Kbp
                                                                                      2528.4Mbp
                                                                                      2808.0
                                                                                      107.26
                                                                                      17.24
                                                                                      81.0%
                                                                                      KSP155.assemble_contigs
                                                                                      2.3Kbp
                                                                                      1.3Kbp
                                                                                      310.8K
                                                                                      686.3K
                                                                                      41.8Kbp
                                                                                      2530.8Mbp
                                                                                      2475.0
                                                                                      107.36
                                                                                      17.29
                                                                                      81.1%
                                                                                      KSP224.assemble_contigs
                                                                                      2.4Kbp
                                                                                      1.3Kbp
                                                                                      300.7K
                                                                                      661.2K
                                                                                      63.9Kbp
                                                                                      2554.3Mbp
                                                                                      1794.0
                                                                                      108.13
                                                                                      17.27
                                                                                      81.9%
                                                                                      KSP228.assemble_contigs
                                                                                      2.3Kbp
                                                                                      1.2Kbp
                                                                                      316.0K
                                                                                      696.1K
                                                                                      46.1Kbp
                                                                                      2534.6Mbp
                                                                                      1965.0
                                                                                      106.59
                                                                                      17.39
                                                                                      81.2%
                                                                                      LP6005443_DNA_G08.assemble_contigs
                                                                                      1.2Kbp
                                                                                      0.8Kbp
                                                                                      535.2K
                                                                                      1076.7K
                                                                                      30.3Kbp
                                                                                      2150.8Mbp
                                                                                      1404.0
                                                                                      96.50
                                                                                      15.53
                                                                                      68.7%
                                                                                      SAMEA2580840.assemble_contigs
                                                                                      5.2Kbp
                                                                                      2.7Kbp
                                                                                      149.8K
                                                                                      327.1K
                                                                                      76.0Kbp
                                                                                      2698.9Mbp
                                                                                      1744.0
                                                                                      119.06
                                                                                      19.98
                                                                                      87.4%
                                                                                      + +
                                                                                      + + +
                                                                                      +
                                                                                      + + +
                                                                                      + + + + + +
                                                                                      + +

                                                                                      + Number of Contigs + +

                                                                                      + +

                                                                                      This plot shows the number of contigs found for each assembly, broken + down by length.

                                                                                      + + +
                                                                                      + + +
                                                                                      +
                                                                                      loading..
                                                                                      +
                                                                                      + + + +
                                                                                      + + + +
                                                                                      +
                                                                                      + + + +
                                                                                      + + +
                                                                                      +

                                                                                      BUSCO

                                                                                      +

                                                                                      BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                                      + + + + +
                                                                                      + +

                                                                                      + Lineage: eukaryota_odb10 + +

                                                                                      + + + + +
                                                                                      + + +
                                                                                      +
                                                                                      loading..
                                                                                      +
                                                                                      + + + +
                                                                                      + + +
                                                                                      + + +
                                                                                      + + + + +
                                                                                      + +
                                                                                      +
                                                                                      + + +

                                                                                      + + + + + MultiQC v1.12 + + - Written by Phil Ewels, + available on GitHub. +

                                                                                      +

                                                                                      + This report uses HighCharts, + jQuery, + jQuery UI, + Bootstrap, + FileSaver.js and + clipboard.js. +

                                                                                      +
                                                                                      +
                                                                                      + + + + + + + + + + + + + + From 133992a5cbf10f91c5feb1227f5c7efb1c810eea Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:32:07 +0200 Subject: [PATCH 18/28] Delete temp --- dataAnalysis/multiQC/finalDataset/temp | 1 - 1 file changed, 1 deletion(-) delete mode 100644 dataAnalysis/multiQC/finalDataset/temp diff --git a/dataAnalysis/multiQC/finalDataset/temp b/dataAnalysis/multiQC/finalDataset/temp deleted file mode 100644 index 8b13789..0000000 --- a/dataAnalysis/multiQC/finalDataset/temp +++ /dev/null @@ -1 +0,0 @@ - From acb7b0d34db2ace1b0d3f48ea749bd497874c1d8 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 17 Apr 2022 12:32:23 +0200 Subject: [PATCH 19/28] Delete temp --- dataAnalysis/multiQC/startingDataset/temp | 1 - 1 file changed, 1 deletion(-) delete mode 100644 dataAnalysis/multiQC/startingDataset/temp diff --git a/dataAnalysis/multiQC/startingDataset/temp b/dataAnalysis/multiQC/startingDataset/temp deleted file mode 100644 index 8b13789..0000000 --- a/dataAnalysis/multiQC/startingDataset/temp +++ /dev/null @@ -1 +0,0 @@ - From f69d36de3e1aa8fc68d472ab7d0247d887f75cc9 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sun, 8 May 2022 12:53:35 +0200 Subject: [PATCH 20/28] Delete dataAnalysis directory --- dataAnalysis/JupyterNotebooks/test | 1 - .../multiQC/finalDataset/BantuNC_report.html | 6068 ----------------- .../multiQC/finalDataset/CARF_report.html | 6068 ----------------- .../multiQC/finalDataset/CWNC_report.html | 6068 ----------------- .../multiQC/finalDataset/EAAA_report.html | 6068 ----------------- .../multiQC/finalDataset/EANS_report.html | 6068 ----------------- .../multiQC/finalDataset/FWNC_report.html | 6068 ----------------- .../multiQC/finalDataset/KS_report.html | 6068 ----------------- .../startingDataset/Bantumultiqc_report.html | 5290 -------------- .../startingDataset/CARFmultiqc_report.html | 5830 ---------------- .../startingDataset/CWNCmultiqc_report.html | 5290 -------------- .../startingDataset/EAAAmultiqc_report.html | 5290 -------------- .../startingDataset/EANSmultiqc_report.html | 5248 -------------- .../startingDataset/FWNCmultiqc_report.html | 5290 -------------- .../KhoeSanmultiqc_report.html | 5248 -------------- 15 files changed, 79963 deletions(-) delete mode 100644 dataAnalysis/JupyterNotebooks/test delete mode 100644 dataAnalysis/multiQC/finalDataset/BantuNC_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/CARF_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/CWNC_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/EAAA_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/EANS_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/FWNC_report.html delete mode 100644 dataAnalysis/multiQC/finalDataset/KS_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/Bantumultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/CARFmultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/CWNCmultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/EAAAmultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/EANSmultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/FWNCmultiqc_report.html delete mode 100644 dataAnalysis/multiQC/startingDataset/KhoeSanmultiqc_report.html diff --git a/dataAnalysis/JupyterNotebooks/test b/dataAnalysis/JupyterNotebooks/test deleted file mode 100644 index 8b13789..0000000 --- a/dataAnalysis/JupyterNotebooks/test +++ /dev/null @@ -1 +0,0 @@ - diff --git a/dataAnalysis/multiQC/finalDataset/BantuNC_report.html b/dataAnalysis/multiQC/finalDataset/BantuNC_report.html deleted file mode 100644 index 1ea1c75..0000000 --- a/dataAnalysis/multiQC/finalDataset/BantuNC_report.html +++ /dev/null @@ -1,6068 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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                                                                                            - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                            - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                            - Bioinformatics (2016)
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                                                                                            This report was generated using MultiQC, version 1.12

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                                                                                            You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                            For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                            - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                            - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                            - Bioinformatics (2016)
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                                                                                            Report - - generated on 2022-02-15, 04:21 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/BantuNC/logs/f9/ba543ed80482b3e6a815c43ab8edd7

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                                                                                            General Statistics

                                                                                            - - - - - - - - - - - Showing 35/35 rows and 2/2 columns. - -
                                                                                            -
                                                                                            - -
                                                                                            Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                            LP6005441_DNA_F01.assemble_contigs
                                                                                            1.1Kbp
                                                                                            1957.2Mbp
                                                                                            LP6005443_DNA_A01.assemble_contigs
                                                                                            1.3Kbp
                                                                                            2182.1Mbp
                                                                                            LP6005443_DNA_E02.assemble_contigs
                                                                                            1.2Kbp
                                                                                            2111.6Mbp
                                                                                            LP6005443_DNA_G02.assemble_contigs
                                                                                            1.1Kbp
                                                                                            2006.5Mbp
                                                                                            NA19028.assemble_contigs
                                                                                            8.0Kbp
                                                                                            2719.7Mbp
                                                                                            NA19038.assemble_contigs
                                                                                            8.2Kbp
                                                                                            2703.8Mbp
                                                                                            NA19309.assemble_contigs
                                                                                            8.4Kbp
                                                                                            2751.0Mbp
                                                                                            NA19317.assemble_contigs
                                                                                            8.4Kbp
                                                                                            2721.0Mbp
                                                                                            NA19318.assemble_contigs
                                                                                            11.0Kbp
                                                                                            2749.5Mbp
                                                                                            NA19328.assemble_contigs
                                                                                            12.3Kbp
                                                                                            2729.4Mbp
                                                                                            NA19332.assemble_contigs
                                                                                            8.5Kbp
                                                                                            2706.5Mbp
                                                                                            NA19350.assemble_contigs
                                                                                            7.8Kbp
                                                                                            2720.1Mbp
                                                                                            NA19372.assemble_contigs
                                                                                            9.8Kbp
                                                                                            2749.7Mbp
                                                                                            NA19380.assemble_contigs
                                                                                            7.9Kbp
                                                                                            2719.0Mbp
                                                                                            NA19385.assemble_contigs
                                                                                            8.1Kbp
                                                                                            2721.1Mbp
                                                                                            NA19434.assemble_contigs
                                                                                            9.9Kbp
                                                                                            2732.8Mbp
                                                                                            NA19448.assemble_contigs
                                                                                            9.5Kbp
                                                                                            2750.4Mbp
                                                                                            NA19461.assemble_contigs
                                                                                            9.8Kbp
                                                                                            2751.1Mbp
                                                                                            NA19463.assemble_contigs
                                                                                            8.2Kbp
                                                                                            2708.0Mbp
                                                                                            NA19467.assemble_contigs
                                                                                            9.7Kbp
                                                                                            2736.1Mbp
                                                                                            NA19471.assemble_contigs
                                                                                            9.5Kbp
                                                                                            2737.2Mbp
                                                                                            NA19473.assemble_contigs
                                                                                            9.2Kbp
                                                                                            2737.4Mbp
                                                                                            SAMEA2580844.assemble_contigs
                                                                                            6.1Kbp
                                                                                            2716.4Mbp
                                                                                            SAMEA2580845.assemble_contigs
                                                                                            5.6Kbp
                                                                                            2709.8Mbp
                                                                                            SAMEA2580848.assemble_contigs
                                                                                            5.8Kbp
                                                                                            2712.7Mbp
                                                                                            SAMEA2580849.assemble_contigs
                                                                                            9.5Kbp
                                                                                            2730.6Mbp
                                                                                            SAMEA2580852.assemble_contigs
                                                                                            5.8Kbp
                                                                                            2712.1Mbp
                                                                                            SAMEA2580853.assemble_contigs
                                                                                            5.7Kbp
                                                                                            2712.8Mbp
                                                                                            SAMEA2580854.assemble_contigs
                                                                                            5.9Kbp
                                                                                            2713.3Mbp
                                                                                            SAMEA2580855.assemble_contigs
                                                                                            6.0Kbp
                                                                                            2715.6Mbp
                                                                                            SAMEA2580856.assemble_contigs
                                                                                            5.7Kbp
                                                                                            2716.2Mbp
                                                                                            SAMEA2580858.assemble_contigs
                                                                                            2.0Kbp
                                                                                            2522.0Mbp
                                                                                            SAMEA2580859.assemble_contigs
                                                                                            3.9Kbp
                                                                                            2691.3Mbp
                                                                                            SAMEA2580861.assemble_contigs
                                                                                            2.1Kbp
                                                                                            2548.3Mbp
                                                                                            SAMEA2580862.assemble_contigs
                                                                                            2.0Kbp
                                                                                            2506.8Mbp
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                                                                                            - - -
                                                                                            -

                                                                                            QUAST

                                                                                            -

                                                                                            QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                            - -

                                                                                            - Assembly Statistics - -

                                                                                            - - - - -
                                                                                            - - - - - - - - - Showing 35/35 rows and 10/10 columns. - -
                                                                                            -
                                                                                            - -
                                                                                            Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                            LP6005441_DNA_F01.assemble_contigs
                                                                                            1.1Kbp
                                                                                            0.7Kbp
                                                                                            600.4K
                                                                                            1159.4K
                                                                                            11.9Kbp
                                                                                            1957.2Mbp
                                                                                            1030.0
                                                                                            82.73
                                                                                            13.15
                                                                                            62.5%
                                                                                            LP6005443_DNA_A01.assemble_contigs
                                                                                            1.3Kbp
                                                                                            0.8Kbp
                                                                                            512.1K
                                                                                            1043.4K
                                                                                            20.6Kbp
                                                                                            2182.1Mbp
                                                                                            1279.0
                                                                                            85.30
                                                                                            13.89
                                                                                            69.7%
                                                                                            LP6005443_DNA_E02.assemble_contigs
                                                                                            1.2Kbp
                                                                                            0.8Kbp
                                                                                            544.7K
                                                                                            1088.8K
                                                                                            23.9Kbp
                                                                                            2111.6Mbp
                                                                                            1209.0
                                                                                            85.25
                                                                                            14.03
                                                                                            67.4%
                                                                                            LP6005443_DNA_G02.assemble_contigs
                                                                                            1.1Kbp
                                                                                            0.8Kbp
                                                                                            570.5K
                                                                                            1120.9K
                                                                                            16.6Kbp
                                                                                            2006.5Mbp
                                                                                            973.0
                                                                                            85.70
                                                                                            13.81
                                                                                            64.1%
                                                                                            NA19028.assemble_contigs
                                                                                            8.0Kbp
                                                                                            4.1Kbp
                                                                                            97.7K
                                                                                            214.8K
                                                                                            113.8Kbp
                                                                                            2719.7Mbp
                                                                                            1547.0
                                                                                            107.83
                                                                                            21.03
                                                                                            88.3%
                                                                                            NA19038.assemble_contigs
                                                                                            8.2Kbp
                                                                                            4.2Kbp
                                                                                            95.3K
                                                                                            210.0K
                                                                                            118.3Kbp
                                                                                            2703.8Mbp
                                                                                            1474.0
                                                                                            107.51
                                                                                            21.06
                                                                                            87.8%
                                                                                            NA19309.assemble_contigs
                                                                                            8.4Kbp
                                                                                            4.3Kbp
                                                                                            93.7K
                                                                                            206.8K
                                                                                            115.6Kbp
                                                                                            2751.0Mbp
                                                                                            1912.0
                                                                                            110.33
                                                                                            24.37
                                                                                            89.0%
                                                                                            NA19317.assemble_contigs
                                                                                            8.4Kbp
                                                                                            4.3Kbp
                                                                                            93.0K
                                                                                            205.0K
                                                                                            106.1Kbp
                                                                                            2721.0Mbp
                                                                                            1600.0
                                                                                            107.81
                                                                                            21.14
                                                                                            88.4%
                                                                                            NA19318.assemble_contigs
                                                                                            11.0Kbp
                                                                                            5.7Kbp
                                                                                            73.0K
                                                                                            159.6K
                                                                                            129.2Kbp
                                                                                            2749.5Mbp
                                                                                            1901.0
                                                                                            110.76
                                                                                            25.07
                                                                                            89.2%
                                                                                            NA19328.assemble_contigs
                                                                                            12.3Kbp
                                                                                            6.3Kbp
                                                                                            64.3K
                                                                                            141.2K
                                                                                            143.3Kbp
                                                                                            2729.4Mbp
                                                                                            1833.0
                                                                                            111.62
                                                                                            24.98
                                                                                            88.6%
                                                                                            NA19332.assemble_contigs
                                                                                            8.5Kbp
                                                                                            4.4Kbp
                                                                                            92.4K
                                                                                            203.3K
                                                                                            102.1Kbp
                                                                                            2706.5Mbp
                                                                                            1610.0
                                                                                            107.74
                                                                                            21.15
                                                                                            87.9%
                                                                                            NA19350.assemble_contigs
                                                                                            7.8Kbp
                                                                                            4.0Kbp
                                                                                            100.2K
                                                                                            220.7K
                                                                                            95.2Kbp
                                                                                            2720.1Mbp
                                                                                            1580.0
                                                                                            107.41
                                                                                            21.03
                                                                                            88.3%
                                                                                            NA19372.assemble_contigs
                                                                                            9.8Kbp
                                                                                            5.0Kbp
                                                                                            81.2K
                                                                                            178.9K
                                                                                            151.6Kbp
                                                                                            2749.7Mbp
                                                                                            1896.0
                                                                                            111.22
                                                                                            24.84
                                                                                            89.1%
                                                                                            NA19380.assemble_contigs
                                                                                            7.9Kbp
                                                                                            4.1Kbp
                                                                                            99.1K
                                                                                            218.0K
                                                                                            100.3Kbp
                                                                                            2719.0Mbp
                                                                                            1522.0
                                                                                            107.32
                                                                                            21.02
                                                                                            88.2%
                                                                                            NA19385.assemble_contigs
                                                                                            8.1Kbp
                                                                                            4.2Kbp
                                                                                            97.0K
                                                                                            213.5K
                                                                                            129.6Kbp
                                                                                            2721.1Mbp
                                                                                            1571.0
                                                                                            107.94
                                                                                            21.15
                                                                                            88.3%
                                                                                            NA19434.assemble_contigs
                                                                                            9.9Kbp
                                                                                            5.1Kbp
                                                                                            80.3K
                                                                                            176.5K
                                                                                            118.9Kbp
                                                                                            2732.8Mbp
                                                                                            1785.0
                                                                                            109.77
                                                                                            24.53
                                                                                            88.5%
                                                                                            NA19448.assemble_contigs
                                                                                            9.5Kbp
                                                                                            4.9Kbp
                                                                                            83.2K
                                                                                            183.6K
                                                                                            132.2Kbp
                                                                                            2750.4Mbp
                                                                                            1947.0
                                                                                            111.19
                                                                                            24.72
                                                                                            89.1%
                                                                                            NA19461.assemble_contigs
                                                                                            9.8Kbp
                                                                                            5.1Kbp
                                                                                            81.5K
                                                                                            178.7K
                                                                                            114.8Kbp
                                                                                            2751.1Mbp
                                                                                            1891.0
                                                                                            110.49
                                                                                            24.73
                                                                                            89.1%
                                                                                            NA19463.assemble_contigs
                                                                                            8.2Kbp
                                                                                            4.2Kbp
                                                                                            95.9K
                                                                                            210.7K
                                                                                            158.2Kbp
                                                                                            2708.0Mbp
                                                                                            1628.0
                                                                                            108.24
                                                                                            21.00
                                                                                            87.9%
                                                                                            NA19467.assemble_contigs
                                                                                            9.7Kbp
                                                                                            5.0Kbp
                                                                                            81.3K
                                                                                            178.7K
                                                                                            134.5Kbp
                                                                                            2736.1Mbp
                                                                                            1958.0
                                                                                            110.66
                                                                                            24.60
                                                                                            88.6%
                                                                                            NA19471.assemble_contigs
                                                                                            9.5Kbp
                                                                                            4.9Kbp
                                                                                            84.1K
                                                                                            183.9K
                                                                                            120.4Kbp
                                                                                            2737.2Mbp
                                                                                            1952.0
                                                                                            111.47
                                                                                            24.82
                                                                                            88.6%
                                                                                            NA19473.assemble_contigs
                                                                                            9.2Kbp
                                                                                            4.8Kbp
                                                                                            86.0K
                                                                                            188.1K
                                                                                            121.2Kbp
                                                                                            2737.4Mbp
                                                                                            1836.0
                                                                                            110.59
                                                                                            24.72
                                                                                            88.6%
                                                                                            SAMEA2580844.assemble_contigs
                                                                                            6.1Kbp
                                                                                            3.2Kbp
                                                                                            130.0K
                                                                                            283.5K
                                                                                            79.3Kbp
                                                                                            2716.4Mbp
                                                                                            1575.0
                                                                                            111.19
                                                                                            20.63
                                                                                            87.9%
                                                                                            SAMEA2580845.assemble_contigs
                                                                                            5.6Kbp
                                                                                            2.9Kbp
                                                                                            141.3K
                                                                                            308.6K
                                                                                            72.4Kbp
                                                                                            2709.8Mbp
                                                                                            1613.0
                                                                                            110.68
                                                                                            19.81
                                                                                            87.7%
                                                                                            SAMEA2580848.assemble_contigs
                                                                                            5.8Kbp
                                                                                            3.0Kbp
                                                                                            136.1K
                                                                                            297.5K
                                                                                            83.7Kbp
                                                                                            2712.7Mbp
                                                                                            1670.0
                                                                                            109.22
                                                                                            19.60
                                                                                            87.8%
                                                                                            SAMEA2580849.assemble_contigs
                                                                                            9.5Kbp
                                                                                            4.8Kbp
                                                                                            82.6K
                                                                                            183.4K
                                                                                            118.6Kbp
                                                                                            2730.6Mbp
                                                                                            1491.0
                                                                                            110.00
                                                                                            24.33
                                                                                            88.4%
                                                                                            SAMEA2580852.assemble_contigs
                                                                                            5.8Kbp
                                                                                            3.0Kbp
                                                                                            135.9K
                                                                                            296.7K
                                                                                            81.3Kbp
                                                                                            2712.1Mbp
                                                                                            1581.0
                                                                                            108.18
                                                                                            19.49
                                                                                            87.8%
                                                                                            SAMEA2580853.assemble_contigs
                                                                                            5.7Kbp
                                                                                            3.0Kbp
                                                                                            138.4K
                                                                                            302.0K
                                                                                            76.7Kbp
                                                                                            2712.8Mbp
                                                                                            1632.0
                                                                                            108.50
                                                                                            19.47
                                                                                            87.8%
                                                                                            SAMEA2580854.assemble_contigs
                                                                                            5.9Kbp
                                                                                            3.1Kbp
                                                                                            134.3K
                                                                                            293.5K
                                                                                            82.7Kbp
                                                                                            2713.3Mbp
                                                                                            1702.0
                                                                                            108.29
                                                                                            19.58
                                                                                            87.9%
                                                                                            SAMEA2580855.assemble_contigs
                                                                                            6.0Kbp
                                                                                            3.1Kbp
                                                                                            132.4K
                                                                                            288.8K
                                                                                            74.6Kbp
                                                                                            2715.6Mbp
                                                                                            1694.0
                                                                                            107.96
                                                                                            19.53
                                                                                            87.9%
                                                                                            SAMEA2580856.assemble_contigs
                                                                                            5.7Kbp
                                                                                            3.0Kbp
                                                                                            137.9K
                                                                                            302.0K
                                                                                            74.1Kbp
                                                                                            2716.2Mbp
                                                                                            1613.0
                                                                                            107.93
                                                                                            19.73
                                                                                            87.9%
                                                                                            SAMEA2580858.assemble_contigs
                                                                                            2.0Kbp
                                                                                            1.1Kbp
                                                                                            372.8K
                                                                                            791.7K
                                                                                            35.8Kbp
                                                                                            2522.0Mbp
                                                                                            1391.0
                                                                                            103.45
                                                                                            15.93
                                                                                            80.4%
                                                                                            SAMEA2580859.assemble_contigs
                                                                                            3.9Kbp
                                                                                            2.0Kbp
                                                                                            200.2K
                                                                                            439.3K
                                                                                            73.7Kbp
                                                                                            2691.3Mbp
                                                                                            1697.0
                                                                                            105.49
                                                                                            18.13
                                                                                            86.6%
                                                                                            SAMEA2580861.assemble_contigs
                                                                                            2.1Kbp
                                                                                            1.2Kbp
                                                                                            353.1K
                                                                                            752.6K
                                                                                            29.3Kbp
                                                                                            2548.3Mbp
                                                                                            1435.0
                                                                                            104.40
                                                                                            15.76
                                                                                            81.4%
                                                                                            SAMEA2580862.assemble_contigs
                                                                                            2.0Kbp
                                                                                            1.1Kbp
                                                                                            375.1K
                                                                                            796.0K
                                                                                            36.7Kbp
                                                                                            2506.8Mbp
                                                                                            1423.0
                                                                                            104.43
                                                                                            15.59
                                                                                            80.0%
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                                                                                            - Number of Contigs - -

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                                                                                            This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                            -

                                                                                            BUSCO

                                                                                            -

                                                                                            BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

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                                                                                            - Lineage: eukaryota_odb10 - -

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                                                                                            - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

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                                                                                            - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                  - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                  - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                  - Bioinformatics (2016)
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                                                                                                  About MultiQC

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                                                                                                  This report was generated using MultiQC, version 1.12

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                                                                                                  You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                  For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                                  You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

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                                                                                                  MultiQC is published in Bioinformatics:

                                                                                                  -
                                                                                                  - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                  - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                  - Bioinformatics (2016)
                                                                                                  - doi: 10.1093/bioinformatics/btw354
                                                                                                  - PMID: 27312411 -
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                                                                                                  - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                  -

                                                                                                  Report - - generated on 2022-02-15, 04:06 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/CARF/logs/a0/1ba21958406cff81a43994c1c29682

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                                                                                                  General Statistics

                                                                                                  - - - - - - - - - - - Showing 22/22 rows and 2/2 columns. - -
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                                                                                                  Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                  LP6005441_DNA_G02.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  2060.9Mbp
                                                                                                  LP6005441_DNA_H02.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  2057.6Mbp
                                                                                                  LP6005592_DNA_C03.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  1963.4Mbp
                                                                                                  SAMEA2580802.assemble_contigs
                                                                                                  3.9Kbp
                                                                                                  2697.1Mbp
                                                                                                  SAMEA2580803.assemble_contigs
                                                                                                  5.9Kbp
                                                                                                  2713.1Mbp
                                                                                                  SAMEA2580807.assemble_contigs
                                                                                                  5.9Kbp
                                                                                                  2712.8Mbp
                                                                                                  SAMEA2580809.assemble_contigs
                                                                                                  9.2Kbp
                                                                                                  2737.4Mbp
                                                                                                  SAMEA2580813.assemble_contigs
                                                                                                  5.7Kbp
                                                                                                  2713.8Mbp
                                                                                                  SAMEA2580815.assemble_contigs
                                                                                                  4.3Kbp
                                                                                                  2703.7Mbp
                                                                                                  SAMEA2580816.assemble_contigs
                                                                                                  5.1Kbp
                                                                                                  2688.7Mbp
                                                                                                  SAMEA2580818.assemble_contigs
                                                                                                  5.6Kbp
                                                                                                  2684.2Mbp
                                                                                                  SAMEA2580819.assemble_contigs
                                                                                                  5.5Kbp
                                                                                                  2688.3Mbp
                                                                                                  SAMEA2580820.assemble_contigs
                                                                                                  5.4Kbp
                                                                                                  2688.1Mbp
                                                                                                  SAMEA2580821.assemble_contigs
                                                                                                  3.5Kbp
                                                                                                  2692.6Mbp
                                                                                                  SAMEA2580822.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  2704.2Mbp
                                                                                                  SAMEA2580823.assemble_contigs
                                                                                                  5.0Kbp
                                                                                                  2703.5Mbp
                                                                                                  SAMEA2580830.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  2704.0Mbp
                                                                                                  SAMEA2580831.assemble_contigs
                                                                                                  6.0Kbp
                                                                                                  2699.3Mbp
                                                                                                  SAMEA2580834.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  2703.3Mbp
                                                                                                  SAMEA2580836.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  2703.9Mbp
                                                                                                  SAMEA3506072.assemble_contigs
                                                                                                  9.2Kbp
                                                                                                  2737.7Mbp
                                                                                                  SAMEA3506073.assemble_contigs
                                                                                                  7.8Kbp
                                                                                                  2708.6Mbp
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                                                                                                  QUAST

                                                                                                  -

                                                                                                  QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                                  - Assembly Statistics - -

                                                                                                  - - - - -
                                                                                                  - - - - - - - - - Showing 22/22 rows and 10/10 columns. - -
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                                                                                                  Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                  LP6005441_DNA_G02.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  0.8Kbp
                                                                                                  573.5K
                                                                                                  1127.4K
                                                                                                  13.0Kbp
                                                                                                  2060.9Mbp
                                                                                                  1144.0
                                                                                                  88.07
                                                                                                  14.19
                                                                                                  65.8%
                                                                                                  LP6005441_DNA_H02.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  0.8Kbp
                                                                                                  577.3K
                                                                                                  1133.2K
                                                                                                  17.3Kbp
                                                                                                  2057.6Mbp
                                                                                                  1198.0
                                                                                                  88.37
                                                                                                  14.18
                                                                                                  65.7%
                                                                                                  LP6005592_DNA_C03.assemble_contigs
                                                                                                  1.1Kbp
                                                                                                  0.7Kbp
                                                                                                  594.5K
                                                                                                  1150.1K
                                                                                                  12.9Kbp
                                                                                                  1963.4Mbp
                                                                                                  1052.0
                                                                                                  90.42
                                                                                                  14.00
                                                                                                  62.7%
                                                                                                  SAMEA2580802.assemble_contigs
                                                                                                  3.9Kbp
                                                                                                  2.1Kbp
                                                                                                  196.9K
                                                                                                  432.3K
                                                                                                  55.3Kbp
                                                                                                  2697.1Mbp
                                                                                                  1728.0
                                                                                                  113.06
                                                                                                  19.97
                                                                                                  86.7%
                                                                                                  SAMEA2580803.assemble_contigs
                                                                                                  5.9Kbp
                                                                                                  3.1Kbp
                                                                                                  134.9K
                                                                                                  294.0K
                                                                                                  63.9Kbp
                                                                                                  2713.1Mbp
                                                                                                  1728.0
                                                                                                  114.73
                                                                                                  20.86
                                                                                                  87.8%
                                                                                                  SAMEA2580807.assemble_contigs
                                                                                                  5.9Kbp
                                                                                                  3.1Kbp
                                                                                                  133.6K
                                                                                                  291.5K
                                                                                                  66.8Kbp
                                                                                                  2712.8Mbp
                                                                                                  1877.0
                                                                                                  114.54
                                                                                                  20.80
                                                                                                  87.8%
                                                                                                  SAMEA2580809.assemble_contigs
                                                                                                  9.2Kbp
                                                                                                  4.7Kbp
                                                                                                  86.2K
                                                                                                  189.8K
                                                                                                  124.1Kbp
                                                                                                  2737.4Mbp
                                                                                                  1414.0
                                                                                                  113.70
                                                                                                  25.59
                                                                                                  88.6%
                                                                                                  SAMEA2580813.assemble_contigs
                                                                                                  5.7Kbp
                                                                                                  3.0Kbp
                                                                                                  139.3K
                                                                                                  303.6K
                                                                                                  60.5Kbp
                                                                                                  2713.8Mbp
                                                                                                  1793.0
                                                                                                  114.39
                                                                                                  20.69
                                                                                                  87.8%
                                                                                                  SAMEA2580815.assemble_contigs
                                                                                                  4.3Kbp
                                                                                                  2.3Kbp
                                                                                                  182.9K
                                                                                                  399.0K
                                                                                                  53.6Kbp
                                                                                                  2703.7Mbp
                                                                                                  1770.0
                                                                                                  113.14
                                                                                                  20.02
                                                                                                  87.1%
                                                                                                  SAMEA2580816.assemble_contigs
                                                                                                  5.1Kbp
                                                                                                  2.7Kbp
                                                                                                  152.8K
                                                                                                  333.2K
                                                                                                  62.1Kbp
                                                                                                  2688.7Mbp
                                                                                                  1699.0
                                                                                                  112.17
                                                                                                  18.37
                                                                                                  87.0%
                                                                                                  SAMEA2580818.assemble_contigs
                                                                                                  5.6Kbp
                                                                                                  2.9Kbp
                                                                                                  140.3K
                                                                                                  306.5K
                                                                                                  79.1Kbp
                                                                                                  2684.2Mbp
                                                                                                  1547.0
                                                                                                  111.63
                                                                                                  18.19
                                                                                                  87.0%
                                                                                                  SAMEA2580819.assemble_contigs
                                                                                                  5.5Kbp
                                                                                                  2.9Kbp
                                                                                                  140.9K
                                                                                                  308.1K
                                                                                                  69.7Kbp
                                                                                                  2688.3Mbp
                                                                                                  1656.0
                                                                                                  113.09
                                                                                                  18.59
                                                                                                  87.1%
                                                                                                  SAMEA2580820.assemble_contigs
                                                                                                  5.4Kbp
                                                                                                  2.8Kbp
                                                                                                  143.9K
                                                                                                  314.4K
                                                                                                  64.1Kbp
                                                                                                  2688.1Mbp
                                                                                                  1567.0
                                                                                                  112.72
                                                                                                  18.42
                                                                                                  87.1%
                                                                                                  SAMEA2580821.assemble_contigs
                                                                                                  3.5Kbp
                                                                                                  1.9Kbp
                                                                                                  218.6K
                                                                                                  478.2K
                                                                                                  65.1Kbp
                                                                                                  2692.6Mbp
                                                                                                  1615.0
                                                                                                  112.56
                                                                                                  19.92
                                                                                                  86.4%
                                                                                                  SAMEA2580822.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  3.0Kbp
                                                                                                  136.6K
                                                                                                  298.3K
                                                                                                  73.7Kbp
                                                                                                  2704.2Mbp
                                                                                                  1685.0
                                                                                                  113.64
                                                                                                  19.52
                                                                                                  87.6%
                                                                                                  SAMEA2580823.assemble_contigs
                                                                                                  5.0Kbp
                                                                                                  2.6Kbp
                                                                                                  159.0K
                                                                                                  346.5K
                                                                                                  60.7Kbp
                                                                                                  2703.5Mbp
                                                                                                  1731.0
                                                                                                  113.67
                                                                                                  20.10
                                                                                                  87.3%
                                                                                                  SAMEA2580830.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  3.0Kbp
                                                                                                  135.8K
                                                                                                  296.6K
                                                                                                  68.4Kbp
                                                                                                  2704.0Mbp
                                                                                                  1681.0
                                                                                                  115.61
                                                                                                  19.82
                                                                                                  87.6%
                                                                                                  SAMEA2580831.assemble_contigs
                                                                                                  6.0Kbp
                                                                                                  3.1Kbp
                                                                                                  130.5K
                                                                                                  284.7K
                                                                                                  69.9Kbp
                                                                                                  2699.3Mbp
                                                                                                  1641.0
                                                                                                  116.42
                                                                                                  21.34
                                                                                                  87.4%
                                                                                                  SAMEA2580834.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  3.0Kbp
                                                                                                  135.5K
                                                                                                  296.0K
                                                                                                  61.8Kbp
                                                                                                  2703.3Mbp
                                                                                                  1675.0
                                                                                                  115.94
                                                                                                  19.81
                                                                                                  87.6%
                                                                                                  SAMEA2580836.assemble_contigs
                                                                                                  5.8Kbp
                                                                                                  3.0Kbp
                                                                                                  135.6K
                                                                                                  296.2K
                                                                                                  66.3Kbp
                                                                                                  2703.9Mbp
                                                                                                  1723.0
                                                                                                  115.54
                                                                                                  19.78
                                                                                                  87.6%
                                                                                                  SAMEA3506072.assemble_contigs
                                                                                                  9.2Kbp
                                                                                                  4.7Kbp
                                                                                                  85.7K
                                                                                                  188.9K
                                                                                                  109.5Kbp
                                                                                                  2737.7Mbp
                                                                                                  1518.0
                                                                                                  114.24
                                                                                                  25.36
                                                                                                  88.7%
                                                                                                  SAMEA3506073.assemble_contigs
                                                                                                  7.8Kbp
                                                                                                  4.0Kbp
                                                                                                  100.0K
                                                                                                  221.2K
                                                                                                  103.6Kbp
                                                                                                  2708.6Mbp
                                                                                                  1473.0
                                                                                                  112.68
                                                                                                  22.13
                                                                                                  87.9%
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                                                                                                  - Number of Contigs - -

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                                                                                                  This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                  BUSCO

                                                                                                  -

                                                                                                  BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                                                  - - - - -
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                                                                                                  - Lineage: eukaryota_odb10 - -

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                                                                                                        - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                        - Bioinformatics (2016)
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                                                                                                        MultiQC is published in Bioinformatics:

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                                                                                                        - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                        - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                        - Bioinformatics (2016)
                                                                                                        - doi: 10.1093/bioinformatics/btw354
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                                                                                                        - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                        Report - - generated on 2022-02-15, 02:32 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/CWNC/logs/b5/18c58258978a13945eda7b1782f5b0

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                                                                                                        General Statistics

                                                                                                        - - - - - - - - - - - Showing 34/34 rows and 2/2 columns. - -
                                                                                                        -
                                                                                                        - -
                                                                                                        Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                        10_150304_L001.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        1904.1Mbp
                                                                                                        12_150304_L004.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        1945.6Mbp
                                                                                                        13_RB103T_C_150611_L007.assemble_contigs
                                                                                                        1.3Kbp
                                                                                                        2097.9Mbp
                                                                                                        18_RB108T_C_150611_L008.assemble_contigs
                                                                                                        1.1Kbp
                                                                                                        1872.0Mbp
                                                                                                        22_150304_L004.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        1984.1Mbp
                                                                                                        27_150304_L003.assemble_contigs
                                                                                                        1.1Kbp
                                                                                                        1879.0Mbp
                                                                                                        28_RB118T_C_150616_L003.assemble_contigs
                                                                                                        1.4Kbp
                                                                                                        2010.9Mbp
                                                                                                        30_RB122T_C_150616_L004.assemble_contigs
                                                                                                        1.4Kbp
                                                                                                        2049.0Mbp
                                                                                                        39_150304_L002.assemble_contigs
                                                                                                        1.3Kbp
                                                                                                        1916.0Mbp
                                                                                                        CB12.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        2693.0Mbp
                                                                                                        CB14.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        2674.9Mbp
                                                                                                        CB15.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        2692.6Mbp
                                                                                                        CB16.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        2689.1Mbp
                                                                                                        CB17.assemble_contigs
                                                                                                        4.9Kbp
                                                                                                        2699.5Mbp
                                                                                                        CB24.assemble_contigs
                                                                                                        6.6Kbp
                                                                                                        2692.1Mbp
                                                                                                        CB29.assemble_contigs
                                                                                                        5.3Kbp
                                                                                                        2698.7Mbp
                                                                                                        CB31.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        2690.9Mbp
                                                                                                        CB32.assemble_contigs
                                                                                                        5.4Kbp
                                                                                                        2682.4Mbp
                                                                                                        CB33.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        2676.9Mbp
                                                                                                        CB7.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        2677.7Mbp
                                                                                                        CF24.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        2689.1Mbp
                                                                                                        CF25.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        2689.5Mbp
                                                                                                        CF26.assemble_contigs
                                                                                                        6.2Kbp
                                                                                                        2680.6Mbp
                                                                                                        CF27.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        2692.9Mbp
                                                                                                        CF30.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        2691.1Mbp
                                                                                                        CF37.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        2688.5Mbp
                                                                                                        CF46.assemble_contigs
                                                                                                        6.2Kbp
                                                                                                        2671.4Mbp
                                                                                                        CF49.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        2673.5Mbp
                                                                                                        CP17.assemble_contigs
                                                                                                        6.0Kbp
                                                                                                        2672.2Mbp
                                                                                                        CP28.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        2691.5Mbp
                                                                                                        CP36.assemble_contigs
                                                                                                        5.8Kbp
                                                                                                        2679.1Mbp
                                                                                                        CP38.assemble_contigs
                                                                                                        5.9Kbp
                                                                                                        2679.4Mbp
                                                                                                        CP40.assemble_contigs
                                                                                                        5.4Kbp
                                                                                                        2698.9Mbp
                                                                                                        CP48.assemble_contigs
                                                                                                        5.9Kbp
                                                                                                        2679.7Mbp
                                                                                                        - - -
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                                                                                                        - - -
                                                                                                        -

                                                                                                        QUAST

                                                                                                        -

                                                                                                        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                                        - -

                                                                                                        - Assembly Statistics - -

                                                                                                        - - - - -
                                                                                                        - - - - - - - - - Showing 34/34 rows and 10/10 columns. - -
                                                                                                        -
                                                                                                        - -
                                                                                                        Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                        10_150304_L001.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        0.8Kbp
                                                                                                        509.6K
                                                                                                        1006.2K
                                                                                                        24.2Kbp
                                                                                                        1904.1Mbp
                                                                                                        1511.0
                                                                                                        99.85
                                                                                                        14.72
                                                                                                        61.4%
                                                                                                        12_150304_L004.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        0.8Kbp
                                                                                                        517.9K
                                                                                                        1023.8K
                                                                                                        14.5Kbp
                                                                                                        1945.6Mbp
                                                                                                        1439.0
                                                                                                        96.38
                                                                                                        14.00
                                                                                                        62.7%
                                                                                                        13_RB103T_C_150611_L007.assemble_contigs
                                                                                                        1.3Kbp
                                                                                                        0.8Kbp
                                                                                                        485.4K
                                                                                                        982.3K
                                                                                                        19.0Kbp
                                                                                                        2097.9Mbp
                                                                                                        1652.0
                                                                                                        99.54
                                                                                                        14.24
                                                                                                        67.4%
                                                                                                        18_RB108T_C_150611_L008.assemble_contigs
                                                                                                        1.1Kbp
                                                                                                        0.8Kbp
                                                                                                        535.4K
                                                                                                        1045.6K
                                                                                                        12.8Kbp
                                                                                                        1872.0Mbp
                                                                                                        1518.0
                                                                                                        95.63
                                                                                                        13.90
                                                                                                        60.4%
                                                                                                        22_150304_L004.assemble_contigs
                                                                                                        1.2Kbp
                                                                                                        0.8Kbp
                                                                                                        500.2K
                                                                                                        997.1K
                                                                                                        15.7Kbp
                                                                                                        1984.1Mbp
                                                                                                        1465.0
                                                                                                        98.21
                                                                                                        14.35
                                                                                                        63.9%
                                                                                                        27_150304_L003.assemble_contigs
                                                                                                        1.1Kbp
                                                                                                        0.8Kbp
                                                                                                        560.6K
                                                                                                        1081.9K
                                                                                                        14.5Kbp
                                                                                                        1879.0Mbp
                                                                                                        1506.0
                                                                                                        95.02
                                                                                                        13.83
                                                                                                        60.7%
                                                                                                        28_RB118T_C_150616_L003.assemble_contigs
                                                                                                        1.4Kbp
                                                                                                        0.9Kbp
                                                                                                        434.6K
                                                                                                        895.1K
                                                                                                        22.1Kbp
                                                                                                        2010.9Mbp
                                                                                                        1559.0
                                                                                                        97.41
                                                                                                        14.07
                                                                                                        64.6%
                                                                                                        30_RB122T_C_150616_L004.assemble_contigs
                                                                                                        1.4Kbp
                                                                                                        0.9Kbp
                                                                                                        419.1K
                                                                                                        876.7K
                                                                                                        23.3Kbp
                                                                                                        2049.0Mbp
                                                                                                        1490.0
                                                                                                        99.56
                                                                                                        14.46
                                                                                                        65.8%
                                                                                                        39_150304_L002.assemble_contigs
                                                                                                        1.3Kbp
                                                                                                        0.8Kbp
                                                                                                        468.8K
                                                                                                        948.5K
                                                                                                        21.3Kbp
                                                                                                        1916.0Mbp
                                                                                                        1350.0
                                                                                                        95.97
                                                                                                        14.24
                                                                                                        61.7%
                                                                                                        CB12.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        3.5Kbp
                                                                                                        117.4K
                                                                                                        257.0K
                                                                                                        75.6Kbp
                                                                                                        2693.0Mbp
                                                                                                        591.0
                                                                                                        104.75
                                                                                                        20.62
                                                                                                        87.4%
                                                                                                        CB14.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        3.4Kbp
                                                                                                        121.2K
                                                                                                        264.7K
                                                                                                        64.8Kbp
                                                                                                        2674.9Mbp
                                                                                                        553.0
                                                                                                        104.47
                                                                                                        20.19
                                                                                                        86.8%
                                                                                                        CB15.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        3.4Kbp
                                                                                                        120.4K
                                                                                                        263.8K
                                                                                                        101.2Kbp
                                                                                                        2692.6Mbp
                                                                                                        628.0
                                                                                                        105.01
                                                                                                        20.66
                                                                                                        87.3%
                                                                                                        CB16.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        3.3Kbp
                                                                                                        123.2K
                                                                                                        270.4K
                                                                                                        72.7Kbp
                                                                                                        2689.1Mbp
                                                                                                        587.0
                                                                                                        104.23
                                                                                                        20.25
                                                                                                        87.2%
                                                                                                        CB17.assemble_contigs
                                                                                                        4.9Kbp
                                                                                                        2.6Kbp
                                                                                                        162.5K
                                                                                                        351.9K
                                                                                                        71.4Kbp
                                                                                                        2699.5Mbp
                                                                                                        725.0
                                                                                                        105.12
                                                                                                        20.73
                                                                                                        87.0%
                                                                                                        CB24.assemble_contigs
                                                                                                        6.6Kbp
                                                                                                        3.4Kbp
                                                                                                        118.0K
                                                                                                        258.4K
                                                                                                        74.9Kbp
                                                                                                        2692.1Mbp
                                                                                                        693.0
                                                                                                        104.59
                                                                                                        20.33
                                                                                                        87.3%
                                                                                                        CB29.assemble_contigs
                                                                                                        5.3Kbp
                                                                                                        2.8Kbp
                                                                                                        148.4K
                                                                                                        322.1K
                                                                                                        65.4Kbp
                                                                                                        2698.7Mbp
                                                                                                        648.0
                                                                                                        104.36
                                                                                                        20.31
                                                                                                        87.1%
                                                                                                        CB31.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        3.4Kbp
                                                                                                        119.7K
                                                                                                        262.3K
                                                                                                        77.5Kbp
                                                                                                        2690.9Mbp
                                                                                                        625.0
                                                                                                        104.44
                                                                                                        20.30
                                                                                                        87.3%
                                                                                                        CB32.assemble_contigs
                                                                                                        5.4Kbp
                                                                                                        2.9Kbp
                                                                                                        145.1K
                                                                                                        315.1K
                                                                                                        78.1Kbp
                                                                                                        2682.4Mbp
                                                                                                        686.0
                                                                                                        104.88
                                                                                                        20.46
                                                                                                        86.7%
                                                                                                        CB33.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        3.4Kbp
                                                                                                        120.9K
                                                                                                        264.3K
                                                                                                        68.5Kbp
                                                                                                        2676.9Mbp
                                                                                                        611.0
                                                                                                        104.70
                                                                                                        20.27
                                                                                                        86.8%
                                                                                                        CB7.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        3.3Kbp
                                                                                                        123.0K
                                                                                                        268.4K
                                                                                                        76.2Kbp
                                                                                                        2677.7Mbp
                                                                                                        607.0
                                                                                                        104.89
                                                                                                        20.30
                                                                                                        86.8%
                                                                                                        CF24.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        3.3Kbp
                                                                                                        121.0K
                                                                                                        265.4K
                                                                                                        78.7Kbp
                                                                                                        2689.1Mbp
                                                                                                        613.0
                                                                                                        104.11
                                                                                                        20.29
                                                                                                        87.2%
                                                                                                        CF25.assemble_contigs
                                                                                                        6.4Kbp
                                                                                                        3.3Kbp
                                                                                                        121.6K
                                                                                                        267.2K
                                                                                                        80.5Kbp
                                                                                                        2689.5Mbp
                                                                                                        594.0
                                                                                                        103.85
                                                                                                        20.40
                                                                                                        87.2%
                                                                                                        CF26.assemble_contigs
                                                                                                        6.2Kbp
                                                                                                        3.3Kbp
                                                                                                        125.2K
                                                                                                        273.5K
                                                                                                        68.5Kbp
                                                                                                        2680.6Mbp
                                                                                                        707.0
                                                                                                        104.61
                                                                                                        20.40
                                                                                                        86.9%
                                                                                                        CF27.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        3.3Kbp
                                                                                                        124.8K
                                                                                                        272.9K
                                                                                                        82.5Kbp
                                                                                                        2692.9Mbp
                                                                                                        679.0
                                                                                                        104.41
                                                                                                        20.39
                                                                                                        87.3%
                                                                                                        CF30.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        3.5Kbp
                                                                                                        117.2K
                                                                                                        256.6K
                                                                                                        70.5Kbp
                                                                                                        2691.1Mbp
                                                                                                        608.0
                                                                                                        103.95
                                                                                                        20.40
                                                                                                        87.3%
                                                                                                        CF37.assemble_contigs
                                                                                                        6.5Kbp
                                                                                                        3.4Kbp
                                                                                                        119.5K
                                                                                                        262.7K
                                                                                                        76.4Kbp
                                                                                                        2688.5Mbp
                                                                                                        590.0
                                                                                                        103.79
                                                                                                        20.26
                                                                                                        87.2%
                                                                                                        CF46.assemble_contigs
                                                                                                        6.2Kbp
                                                                                                        3.3Kbp
                                                                                                        124.6K
                                                                                                        272.1K
                                                                                                        75.1Kbp
                                                                                                        2671.4Mbp
                                                                                                        675.0
                                                                                                        104.22
                                                                                                        20.06
                                                                                                        86.6%
                                                                                                        CF49.assemble_contigs
                                                                                                        6.3Kbp
                                                                                                        3.3Kbp
                                                                                                        124.5K
                                                                                                        272.3K
                                                                                                        74.3Kbp
                                                                                                        2673.5Mbp
                                                                                                        599.0
                                                                                                        103.89
                                                                                                        20.06
                                                                                                        86.7%
                                                                                                        CP17.assemble_contigs
                                                                                                        6.0Kbp
                                                                                                        3.1Kbp
                                                                                                        129.4K
                                                                                                        283.7K
                                                                                                        67.2Kbp
                                                                                                        2672.2Mbp
                                                                                                        670.0
                                                                                                        103.99
                                                                                                        20.23
                                                                                                        86.6%
                                                                                                        CP28.assemble_contigs
                                                                                                        6.7Kbp
                                                                                                        3.5Kbp
                                                                                                        116.8K
                                                                                                        256.1K
                                                                                                        82.6Kbp
                                                                                                        2691.5Mbp
                                                                                                        601.0
                                                                                                        104.29
                                                                                                        20.40
                                                                                                        87.3%
                                                                                                        CP36.assemble_contigs
                                                                                                        5.8Kbp
                                                                                                        3.1Kbp
                                                                                                        135.2K
                                                                                                        293.8K
                                                                                                        60.7Kbp
                                                                                                        2679.1Mbp
                                                                                                        673.0
                                                                                                        104.08
                                                                                                        20.14
                                                                                                        86.7%
                                                                                                        CP38.assemble_contigs
                                                                                                        5.9Kbp
                                                                                                        3.1Kbp
                                                                                                        132.0K
                                                                                                        287.6K
                                                                                                        82.4Kbp
                                                                                                        2679.4Mbp
                                                                                                        627.0
                                                                                                        104.19
                                                                                                        20.17
                                                                                                        86.8%
                                                                                                        CP40.assemble_contigs
                                                                                                        5.4Kbp
                                                                                                        2.9Kbp
                                                                                                        146.4K
                                                                                                        317.4K
                                                                                                        61.1Kbp
                                                                                                        2698.9Mbp
                                                                                                        707.0
                                                                                                        104.61
                                                                                                        20.50
                                                                                                        87.2%
                                                                                                        CP48.assemble_contigs
                                                                                                        5.9Kbp
                                                                                                        3.1Kbp
                                                                                                        133.2K
                                                                                                        290.2K
                                                                                                        71.0Kbp
                                                                                                        2679.7Mbp
                                                                                                        616.0
                                                                                                        104.68
                                                                                                        20.37
                                                                                                        86.7%
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                                                                                                        - -

                                                                                                        - Number of Contigs - -

                                                                                                        - -

                                                                                                        This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                        BUSCO

                                                                                                        -

                                                                                                        BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                                                        - - - - -
                                                                                                        - -

                                                                                                        - Lineage: eukaryota_odb10 - -

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                                                                                                        - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

                                                                                                        -

                                                                                                        - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                              - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                              - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                              - Bioinformatics (2016)
                                                                                                              - doi: 10.1093/bioinformatics/btw354
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                                                                                                              Tool Citations

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                                                                                                              Please remember to cite the tools that you use in your analysis.

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                                                                                                              About MultiQC

                                                                                                              -

                                                                                                              This report was generated using MultiQC, version 1.12

                                                                                                              -

                                                                                                              You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

                                                                                                              -

                                                                                                              For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

                                                                                                              -

                                                                                                              You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

                                                                                                              -

                                                                                                              MultiQC is published in Bioinformatics:

                                                                                                              -
                                                                                                              - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                              - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                              - Bioinformatics (2016)
                                                                                                              - doi: 10.1093/bioinformatics/btw354
                                                                                                              - PMID: 27312411 -
                                                                                                              -
                                                                                                              - -
                                                                                                              - -
                                                                                                              - - -
                                                                                                              - - - -

                                                                                                              - - - - -

                                                                                                              - - - -

                                                                                                              - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

                                                                                                              - - - - - - - - - - - -
                                                                                                              -

                                                                                                              Report - - generated on 2022-02-10, 01:48 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/EAAA/logs/cf/1dc031e6d9977611275531e143d0a5

                                                                                                              - - -
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                                                                                                              - - - - - - - - -
                                                                                                              -

                                                                                                              General Statistics

                                                                                                              - - - - - - - - - - - Showing 5/5 rows and 2/2 columns. - -
                                                                                                              -
                                                                                                              - -
                                                                                                              Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                              LP6005442_DNA_D09.assemble_contigs
                                                                                                              1.1Kbp
                                                                                                              2101.9Mbp
                                                                                                              egpg5305762.assemble_contigs
                                                                                                              1.7Kbp
                                                                                                              2016.7Mbp
                                                                                                              egpg5305920.assemble_contigs
                                                                                                              1.3Kbp
                                                                                                              2070.7Mbp
                                                                                                              egpg5305949.assemble_contigs
                                                                                                              1.3Kbp
                                                                                                              2036.2Mbp
                                                                                                              egpg5305974.assemble_contigs
                                                                                                              1.5Kbp
                                                                                                              2292.4Mbp
                                                                                                              - - -
                                                                                                              - - - - - - -
                                                                                                              - - -
                                                                                                              -

                                                                                                              QUAST

                                                                                                              -

                                                                                                              QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

                                                                                                              - - - - -
                                                                                                              - -

                                                                                                              - Assembly Statistics - -

                                                                                                              - - - - -
                                                                                                              - - - - - - - - - Showing 5/5 rows and 10/10 columns. - -
                                                                                                              -
                                                                                                              - -
                                                                                                              Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                              LP6005442_DNA_D09.assemble_contigs
                                                                                                              1.1Kbp
                                                                                                              0.8Kbp
                                                                                                              597.4K
                                                                                                              1169.3K
                                                                                                              12.6Kbp
                                                                                                              2101.9Mbp
                                                                                                              1063.0
                                                                                                              77.87
                                                                                                              12.51
                                                                                                              67.1%
                                                                                                              egpg5305762.assemble_contigs
                                                                                                              1.7Kbp
                                                                                                              1.0Kbp
                                                                                                              359.1K
                                                                                                              753.9K
                                                                                                              30.8Kbp
                                                                                                              2016.7Mbp
                                                                                                              1504.0
                                                                                                              91.17
                                                                                                              13.97
                                                                                                              64.8%
                                                                                                              egpg5305920.assemble_contigs
                                                                                                              1.3Kbp
                                                                                                              0.9Kbp
                                                                                                              473.3K
                                                                                                              962.7K
                                                                                                              24.5Kbp
                                                                                                              2070.7Mbp
                                                                                                              1454.0
                                                                                                              86.94
                                                                                                              12.59
                                                                                                              66.7%
                                                                                                              egpg5305949.assemble_contigs
                                                                                                              1.3Kbp
                                                                                                              0.8Kbp
                                                                                                              482.7K
                                                                                                              975.3K
                                                                                                              45.4Kbp
                                                                                                              2036.2Mbp
                                                                                                              1581.0
                                                                                                              86.48
                                                                                                              12.03
                                                                                                              65.5%
                                                                                                              egpg5305974.assemble_contigs
                                                                                                              1.5Kbp
                                                                                                              0.9Kbp
                                                                                                              446.3K
                                                                                                              927.8K
                                                                                                              30.1Kbp
                                                                                                              2292.4Mbp
                                                                                                              1672.0
                                                                                                              87.41
                                                                                                              13.45
                                                                                                              73.6%
                                                                                                              - -
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                                                                                                              -
                                                                                                              - - -
                                                                                                              - - - - - -
                                                                                                              - -

                                                                                                              - Number of Contigs - -

                                                                                                              - -

                                                                                                              This plot shows the number of contigs found for each assembly, broken - down by length.

                                                                                                              - - -
                                                                                                              - - -
                                                                                                              -
                                                                                                              loading..
                                                                                                              -
                                                                                                              - - - -
                                                                                                              - - - -
                                                                                                              -
                                                                                                              - - - -
                                                                                                              - - -
                                                                                                              -

                                                                                                              BUSCO

                                                                                                              -

                                                                                                              BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

                                                                                                              - - - - -
                                                                                                              - -

                                                                                                              - Lineage: eukaryota_odb10 - -

                                                                                                              - - - - -
                                                                                                              - - -
                                                                                                              -
                                                                                                              loading..
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                                                                                                              - - - -
                                                                                                              - - -
                                                                                                              - - -
                                                                                                              - - - - -
                                                                                                              - -
                                                                                                              -
                                                                                                              - - -

                                                                                                              - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

                                                                                                              -

                                                                                                              - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

                                                                                                              -
                                                                                                              -
                                                                                                              - - - - - - - - - - - - - - diff --git a/dataAnalysis/multiQC/finalDataset/EANS_report.html b/dataAnalysis/multiQC/finalDataset/EANS_report.html deleted file mode 100644 index 8f4d570..0000000 --- a/dataAnalysis/multiQC/finalDataset/EANS_report.html +++ /dev/null @@ -1,6068 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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                                                                                                                    Note that additional data was saved in multiqc_data when this report was generated.

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                                                                                                                    If you use plots from MultiQC in a publication or presentation, please cite:

                                                                                                                    -
                                                                                                                    - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                    - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                    - Bioinformatics (2016)
                                                                                                                    - doi: 10.1093/bioinformatics/btw354
                                                                                                                    - PMID: 27312411 -
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                                                                                                                    Tool Citations

                                                                                                                    -

                                                                                                                    Please remember to cite the tools that you use in your analysis.

                                                                                                                    -

                                                                                                                    To help with this, you can download publication details of the tools mentioned in this report:

                                                                                                                    -

                                                                                                                    -

                                                                                                                    -
                                                                                                                    - - -
                                                                                                                    -

                                                                                                                    About MultiQC

                                                                                                                    -

                                                                                                                    This report was generated using MultiQC, version 1.12

                                                                                                                    -

                                                                                                                    You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

                                                                                                                    -

                                                                                                                    For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

                                                                                                                    -

                                                                                                                    You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

                                                                                                                    -

                                                                                                                    MultiQC is published in Bioinformatics:

                                                                                                                    -
                                                                                                                    - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                    - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                    - Bioinformatics (2016)
                                                                                                                    - doi: 10.1093/bioinformatics/btw354
                                                                                                                    - PMID: 27312411 -
                                                                                                                    -
                                                                                                                    - -
                                                                                                                    - -
                                                                                                                    - - -
                                                                                                                    - - - -

                                                                                                                    - - - - -

                                                                                                                    - - - -

                                                                                                                    - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

                                                                                                                    - - - - - - - - - - - -
                                                                                                                    -

                                                                                                                    Report - - generated on 2022-02-15, 23:51 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/EANS/logs/98/ab813fde59732ba238f4e66791355b

                                                                                                                    - - -
                                                                                                                    - - - - - - - -
                                                                                                                    - - - - - - - - -
                                                                                                                    -

                                                                                                                    General Statistics

                                                                                                                    - - - - - - - - - - - Showing 18/18 rows and 2/2 columns. - -
                                                                                                                    -
                                                                                                                    - -
                                                                                                                    Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                                    10_UO_113T_150731_L003.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    1884.2Mbp
                                                                                                                    13_UO_134T_150731_L005.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    2074.9Mbp
                                                                                                                    16_UO_142T_150731_L006.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    1935.3Mbp
                                                                                                                    17_UO_144T_150731_L007.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    1974.7Mbp
                                                                                                                    1_UO_005T_150730_L001.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    1925.3Mbp
                                                                                                                    22_UO_045C_150813_L002.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    1943.6Mbp
                                                                                                                    27_UO_072C_150813_L001.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    1999.4Mbp
                                                                                                                    35_UO_090C_150813_L005.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    1912.0Mbp
                                                                                                                    39_UO_098C_150902_L002.assemble_contigs
                                                                                                                    1.7Kbp
                                                                                                                    2181.8Mbp
                                                                                                                    42_UO_105C_150902_L003.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    2035.2Mbp
                                                                                                                    43_UO_106C_150902_L004.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    1878.4Mbp
                                                                                                                    44_UO_107C_150902_L004.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    1873.6Mbp
                                                                                                                    47_UO_115C_150902_L006.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    1989.4Mbp
                                                                                                                    6_UO_069T_150731_L001.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    2055.9Mbp
                                                                                                                    7_UO_071T_150731_L002.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    1914.9Mbp
                                                                                                                    8_UO_074T_150731_L002.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    1864.2Mbp
                                                                                                                    LP6005443_DNA_F06.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    2166.7Mbp
                                                                                                                    egpg5305814.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    2039.1Mbp
                                                                                                                    - - -
                                                                                                                    - - - - - - -
                                                                                                                    - - -
                                                                                                                    -

                                                                                                                    QUAST

                                                                                                                    -

                                                                                                                    QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                                                    - Assembly Statistics - -

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                                                                                                                    - - - - - - - - - Showing 18/18 rows and 10/10 columns. - -
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                                                                                                                    Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                    10_UO_113T_150731_L003.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    0.8Kbp
                                                                                                                    546.5K
                                                                                                                    1056.7K
                                                                                                                    13.2Kbp
                                                                                                                    1884.2Mbp
                                                                                                                    1499.0
                                                                                                                    95.00
                                                                                                                    13.57
                                                                                                                    60.8%
                                                                                                                    13_UO_134T_150731_L005.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.9Kbp
                                                                                                                    478.2K
                                                                                                                    965.2K
                                                                                                                    21.8Kbp
                                                                                                                    2074.9Mbp
                                                                                                                    1535.0
                                                                                                                    98.67
                                                                                                                    14.19
                                                                                                                    66.7%
                                                                                                                    16_UO_142T_150731_L006.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    538.8K
                                                                                                                    1048.9K
                                                                                                                    13.5Kbp
                                                                                                                    1935.3Mbp
                                                                                                                    1530.0
                                                                                                                    95.58
                                                                                                                    13.67
                                                                                                                    62.4%
                                                                                                                    17_UO_144T_150731_L007.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.8Kbp
                                                                                                                    491.4K
                                                                                                                    979.2K
                                                                                                                    15.4Kbp
                                                                                                                    1974.7Mbp
                                                                                                                    1467.0
                                                                                                                    98.24
                                                                                                                    14.18
                                                                                                                    63.6%
                                                                                                                    1_UO_005T_150730_L001.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    497.1K
                                                                                                                    984.2K
                                                                                                                    12.8Kbp
                                                                                                                    1925.3Mbp
                                                                                                                    1691.0
                                                                                                                    97.60
                                                                                                                    14.00
                                                                                                                    62.0%
                                                                                                                    22_UO_045C_150813_L002.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.8Kbp
                                                                                                                    478.2K
                                                                                                                    957.3K
                                                                                                                    15.8Kbp
                                                                                                                    1943.6Mbp
                                                                                                                    1492.0
                                                                                                                    98.15
                                                                                                                    14.30
                                                                                                                    62.5%
                                                                                                                    27_UO_072C_150813_L001.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.8Kbp
                                                                                                                    501.3K
                                                                                                                    994.5K
                                                                                                                    23.5Kbp
                                                                                                                    1999.4Mbp
                                                                                                                    1492.0
                                                                                                                    98.14
                                                                                                                    14.28
                                                                                                                    64.4%
                                                                                                                    35_UO_090C_150813_L005.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    510.7K
                                                                                                                    1002.9K
                                                                                                                    13.6Kbp
                                                                                                                    1912.0Mbp
                                                                                                                    1594.0
                                                                                                                    97.62
                                                                                                                    13.92
                                                                                                                    61.6%
                                                                                                                    39_UO_098C_150902_L002.assemble_contigs
                                                                                                                    1.7Kbp
                                                                                                                    1.0Kbp
                                                                                                                    376.8K
                                                                                                                    805.0K
                                                                                                                    24.9Kbp
                                                                                                                    2181.8Mbp
                                                                                                                    1624.0
                                                                                                                    101.32
                                                                                                                    14.28
                                                                                                                    70.1%
                                                                                                                    42_UO_105C_150902_L003.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.8Kbp
                                                                                                                    508.3K
                                                                                                                    1007.9K
                                                                                                                    21.7Kbp
                                                                                                                    2035.2Mbp
                                                                                                                    1542.0
                                                                                                                    98.82
                                                                                                                    14.17
                                                                                                                    65.5%
                                                                                                                    43_UO_106C_150902_L004.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    0.8Kbp
                                                                                                                    533.7K
                                                                                                                    1035.1K
                                                                                                                    13.2Kbp
                                                                                                                    1878.4Mbp
                                                                                                                    1433.0
                                                                                                                    97.64
                                                                                                                    13.87
                                                                                                                    60.6%
                                                                                                                    44_UO_107C_150902_L004.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    0.8Kbp
                                                                                                                    535.9K
                                                                                                                    1038.0K
                                                                                                                    13.2Kbp
                                                                                                                    1873.6Mbp
                                                                                                                    1552.0
                                                                                                                    97.02
                                                                                                                    13.66
                                                                                                                    60.4%
                                                                                                                    47_UO_115C_150902_L006.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    532.8K
                                                                                                                    1041.7K
                                                                                                                    14.4Kbp
                                                                                                                    1989.4Mbp
                                                                                                                    1536.0
                                                                                                                    96.12
                                                                                                                    13.63
                                                                                                                    64.1%
                                                                                                                    6_UO_069T_150731_L001.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.9Kbp
                                                                                                                    468.4K
                                                                                                                    949.5K
                                                                                                                    18.4Kbp
                                                                                                                    2055.9Mbp
                                                                                                                    1501.0
                                                                                                                    98.67
                                                                                                                    14.34
                                                                                                                    66.1%
                                                                                                                    7_UO_071T_150731_L002.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    516.7K
                                                                                                                    1012.1K
                                                                                                                    13.6Kbp
                                                                                                                    1914.9Mbp
                                                                                                                    1413.0
                                                                                                                    97.86
                                                                                                                    13.75
                                                                                                                    61.7%
                                                                                                                    8_UO_074T_150731_L002.assemble_contigs
                                                                                                                    1.1Kbp
                                                                                                                    0.8Kbp
                                                                                                                    519.1K
                                                                                                                    1015.1K
                                                                                                                    13.8Kbp
                                                                                                                    1864.2Mbp
                                                                                                                    1471.0
                                                                                                                    95.18
                                                                                                                    13.45
                                                                                                                    60.1%
                                                                                                                    LP6005443_DNA_F06.assemble_contigs
                                                                                                                    1.3Kbp
                                                                                                                    0.8Kbp
                                                                                                                    512.7K
                                                                                                                    1044.5K
                                                                                                                    18.4Kbp
                                                                                                                    2166.7Mbp
                                                                                                                    1208.0
                                                                                                                    82.48
                                                                                                                    13.39
                                                                                                                    69.2%
                                                                                                                    egpg5305814.assemble_contigs
                                                                                                                    1.2Kbp
                                                                                                                    0.8Kbp
                                                                                                                    509.6K
                                                                                                                    1020.5K
                                                                                                                    43.5Kbp
                                                                                                                    2039.1Mbp
                                                                                                                    1556.0
                                                                                                                    91.98
                                                                                                                    12.77
                                                                                                                    65.6%
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                                                                                                                    - Number of Contigs - -

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                                                                                                                    This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                    BUSCO

                                                                                                                    -

                                                                                                                    BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

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                                                                                                                    - Lineage: eukaryota_odb10 - -

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                                                                                                                    - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

                                                                                                                    -

                                                                                                                    - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                                          - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                          - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                          - Bioinformatics (2016)
                                                                                                                          - doi: 10.1093/bioinformatics/btw354
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                                                                                                                          About MultiQC

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                                                                                                                          This report was generated using MultiQC, version 1.12

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                                                                                                                          You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                                          For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                                                          You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

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                                                                                                                          MultiQC is published in Bioinformatics:

                                                                                                                          -
                                                                                                                          - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                          - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                          - Bioinformatics (2016)
                                                                                                                          - doi: 10.1093/bioinformatics/btw354
                                                                                                                          - PMID: 27312411 -
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                                                                                                                          - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                          Report - - generated on 2022-02-16, 01:40 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/FWNC/logs/85/dac2781488b5e179cb0386bdd8e0fa

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                                                                                                                          General Statistics

                                                                                                                          - - - - - - - - - - - Showing 35/35 rows and 2/2 columns. - -
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                                                                                                                          Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                                          HG03225.assemble_contigs
                                                                                                                          8.3Kbp
                                                                                                                          2722.4Mbp
                                                                                                                          HG03380.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          2705.7Mbp
                                                                                                                          HG03385.assemble_contigs
                                                                                                                          9.7Kbp
                                                                                                                          2749.9Mbp
                                                                                                                          HG03388.assemble_contigs
                                                                                                                          8.3Kbp
                                                                                                                          2720.8Mbp
                                                                                                                          HG03449.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          2705.0Mbp
                                                                                                                          IAJ0K.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          2673.4Mbp
                                                                                                                          IAM0N.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          2674.2Mbp
                                                                                                                          IAP0Q.assemble_contigs
                                                                                                                          6.5Kbp
                                                                                                                          2694.4Mbp
                                                                                                                          IBJ0M.assemble_contigs
                                                                                                                          6.3Kbp
                                                                                                                          2673.2Mbp
                                                                                                                          IBQ0T.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          2675.8Mbp
                                                                                                                          LP6005441_DNA_F07.assemble_contigs
                                                                                                                          1.0Kbp
                                                                                                                          1948.4Mbp
                                                                                                                          LZP0B.assemble_contigs
                                                                                                                          6.8Kbp
                                                                                                                          2691.8Mbp
                                                                                                                          NA18498.assemble_contigs
                                                                                                                          7.8Kbp
                                                                                                                          2725.2Mbp
                                                                                                                          NA18499.assemble_contigs
                                                                                                                          10.2Kbp
                                                                                                                          2735.3Mbp
                                                                                                                          NA18501.assemble_contigs
                                                                                                                          7.5Kbp
                                                                                                                          2726.0Mbp
                                                                                                                          NA18504.assemble_contigs
                                                                                                                          8.0Kbp
                                                                                                                          2722.1Mbp
                                                                                                                          NA18505.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          2701.5Mbp
                                                                                                                          NA19099.assemble_contigs
                                                                                                                          8.5Kbp
                                                                                                                          2703.3Mbp
                                                                                                                          NA19107.assemble_contigs
                                                                                                                          9.3Kbp
                                                                                                                          2750.0Mbp
                                                                                                                          NA19118.assemble_contigs
                                                                                                                          8.4Kbp
                                                                                                                          2703.0Mbp
                                                                                                                          NA19129.assemble_contigs
                                                                                                                          10.8Kbp
                                                                                                                          2734.4Mbp
                                                                                                                          NA19131.assemble_contigs
                                                                                                                          12.0Kbp
                                                                                                                          2732.8Mbp
                                                                                                                          PAV0Q.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          2693.0Mbp
                                                                                                                          PAZ0V.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          2677.5Mbp
                                                                                                                          PBA0X.assemble_contigs
                                                                                                                          6.8Kbp
                                                                                                                          2692.6Mbp
                                                                                                                          PBC0A.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          2677.5Mbp
                                                                                                                          SAMEA2580885.assemble_contigs
                                                                                                                          4.9Kbp
                                                                                                                          2720.3Mbp
                                                                                                                          SAMEA2580886.assemble_contigs
                                                                                                                          5.8Kbp
                                                                                                                          2719.7Mbp
                                                                                                                          SAMEA2580889.assemble_contigs
                                                                                                                          5.8Kbp
                                                                                                                          2714.4Mbp
                                                                                                                          SAMEA2580891.assemble_contigs
                                                                                                                          5.9Kbp
                                                                                                                          2699.9Mbp
                                                                                                                          SAMEA2580897.assemble_contigs
                                                                                                                          7.9Kbp
                                                                                                                          2726.5Mbp
                                                                                                                          SAMEA3506075.assemble_contigs
                                                                                                                          10.1Kbp
                                                                                                                          2739.4Mbp
                                                                                                                          SAMEA3506076.assemble_contigs
                                                                                                                          10.8Kbp
                                                                                                                          2722.1Mbp
                                                                                                                          SAMEA3506077.assemble_contigs
                                                                                                                          9.2Kbp
                                                                                                                          2740.3Mbp
                                                                                                                          SAMEA3506078.assemble_contigs
                                                                                                                          7.6Kbp
                                                                                                                          2741.2Mbp
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                                                                                                                          QUAST

                                                                                                                          -

                                                                                                                          QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                                                          - Assembly Statistics - -

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                                                                                                                          - - - - - - - - - Showing 35/35 rows and 10/10 columns. - -
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                                                                                                                          Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                          HG03225.assemble_contigs
                                                                                                                          8.3Kbp
                                                                                                                          4.3Kbp
                                                                                                                          94.3K
                                                                                                                          207.7K
                                                                                                                          120.4Kbp
                                                                                                                          2722.4Mbp
                                                                                                                          1692.0
                                                                                                                          109.29
                                                                                                                          21.41
                                                                                                                          88.4%
                                                                                                                          HG03380.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          4.2Kbp
                                                                                                                          96.4K
                                                                                                                          211.8K
                                                                                                                          137.0Kbp
                                                                                                                          2705.7Mbp
                                                                                                                          1587.0
                                                                                                                          109.02
                                                                                                                          21.21
                                                                                                                          87.8%
                                                                                                                          HG03385.assemble_contigs
                                                                                                                          9.7Kbp
                                                                                                                          5.0Kbp
                                                                                                                          82.1K
                                                                                                                          180.5K
                                                                                                                          175.1Kbp
                                                                                                                          2749.9Mbp
                                                                                                                          1838.0
                                                                                                                          111.24
                                                                                                                          24.88
                                                                                                                          89.1%
                                                                                                                          HG03388.assemble_contigs
                                                                                                                          8.3Kbp
                                                                                                                          4.3Kbp
                                                                                                                          94.1K
                                                                                                                          207.5K
                                                                                                                          196.0Kbp
                                                                                                                          2720.8Mbp
                                                                                                                          1697.0
                                                                                                                          109.32
                                                                                                                          21.38
                                                                                                                          88.3%
                                                                                                                          HG03449.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          4.2Kbp
                                                                                                                          96.2K
                                                                                                                          211.4K
                                                                                                                          129.9Kbp
                                                                                                                          2705.0Mbp
                                                                                                                          1573.0
                                                                                                                          109.28
                                                                                                                          21.15
                                                                                                                          87.8%
                                                                                                                          IAJ0K.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          3.3Kbp
                                                                                                                          121.8K
                                                                                                                          266.5K
                                                                                                                          69.7Kbp
                                                                                                                          2673.4Mbp
                                                                                                                          625.0
                                                                                                                          103.44
                                                                                                                          20.09
                                                                                                                          86.7%
                                                                                                                          IAM0N.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          3.3Kbp
                                                                                                                          121.9K
                                                                                                                          266.6K
                                                                                                                          82.8Kbp
                                                                                                                          2674.2Mbp
                                                                                                                          618.0
                                                                                                                          103.26
                                                                                                                          20.09
                                                                                                                          86.7%
                                                                                                                          IAP0Q.assemble_contigs
                                                                                                                          6.5Kbp
                                                                                                                          3.4Kbp
                                                                                                                          119.9K
                                                                                                                          263.0K
                                                                                                                          81.8Kbp
                                                                                                                          2694.4Mbp
                                                                                                                          684.0
                                                                                                                          103.48
                                                                                                                          20.44
                                                                                                                          87.4%
                                                                                                                          IBJ0M.assemble_contigs
                                                                                                                          6.3Kbp
                                                                                                                          3.3Kbp
                                                                                                                          123.3K
                                                                                                                          269.5K
                                                                                                                          73.1Kbp
                                                                                                                          2673.2Mbp
                                                                                                                          626.0
                                                                                                                          103.39
                                                                                                                          20.08
                                                                                                                          86.7%
                                                                                                                          IBQ0T.assemble_contigs
                                                                                                                          6.4Kbp
                                                                                                                          3.3Kbp
                                                                                                                          121.5K
                                                                                                                          266.1K
                                                                                                                          73.7Kbp
                                                                                                                          2675.8Mbp
                                                                                                                          586.0
                                                                                                                          103.15
                                                                                                                          20.18
                                                                                                                          86.8%
                                                                                                                          LP6005441_DNA_F07.assemble_contigs
                                                                                                                          1.0Kbp
                                                                                                                          0.7Kbp
                                                                                                                          665.2K
                                                                                                                          1255.2K
                                                                                                                          13.4Kbp
                                                                                                                          1948.4Mbp
                                                                                                                          1017.0
                                                                                                                          78.10
                                                                                                                          12.64
                                                                                                                          62.2%
                                                                                                                          LZP0B.assemble_contigs
                                                                                                                          6.8Kbp
                                                                                                                          3.5Kbp
                                                                                                                          114.7K
                                                                                                                          251.7K
                                                                                                                          77.6Kbp
                                                                                                                          2691.8Mbp
                                                                                                                          607.0
                                                                                                                          103.48
                                                                                                                          20.42
                                                                                                                          87.4%
                                                                                                                          NA18498.assemble_contigs
                                                                                                                          7.8Kbp
                                                                                                                          4.1Kbp
                                                                                                                          100.6K
                                                                                                                          220.7K
                                                                                                                          114.7Kbp
                                                                                                                          2725.2Mbp
                                                                                                                          1642.0
                                                                                                                          108.34
                                                                                                                          21.29
                                                                                                                          88.4%
                                                                                                                          NA18499.assemble_contigs
                                                                                                                          10.2Kbp
                                                                                                                          5.3Kbp
                                                                                                                          77.9K
                                                                                                                          171.0K
                                                                                                                          167.8Kbp
                                                                                                                          2735.3Mbp
                                                                                                                          1895.0
                                                                                                                          111.11
                                                                                                                          24.87
                                                                                                                          88.6%
                                                                                                                          NA18501.assemble_contigs
                                                                                                                          7.5Kbp
                                                                                                                          3.9Kbp
                                                                                                                          105.1K
                                                                                                                          231.4K
                                                                                                                          101.2Kbp
                                                                                                                          2726.0Mbp
                                                                                                                          1719.0
                                                                                                                          108.86
                                                                                                                          21.32
                                                                                                                          88.3%
                                                                                                                          NA18504.assemble_contigs
                                                                                                                          8.0Kbp
                                                                                                                          4.1Kbp
                                                                                                                          98.2K
                                                                                                                          216.4K
                                                                                                                          118.3Kbp
                                                                                                                          2722.1Mbp
                                                                                                                          1463.0
                                                                                                                          107.57
                                                                                                                          21.28
                                                                                                                          88.3%
                                                                                                                          NA18505.assemble_contigs
                                                                                                                          8.1Kbp
                                                                                                                          4.2Kbp
                                                                                                                          97.1K
                                                                                                                          213.5K
                                                                                                                          93.3Kbp
                                                                                                                          2701.5Mbp
                                                                                                                          1510.0
                                                                                                                          108.11
                                                                                                                          20.98
                                                                                                                          87.7%
                                                                                                                          NA19099.assemble_contigs
                                                                                                                          8.5Kbp
                                                                                                                          4.4Kbp
                                                                                                                          92.2K
                                                                                                                          202.4K
                                                                                                                          101.8Kbp
                                                                                                                          2703.3Mbp
                                                                                                                          1579.0
                                                                                                                          107.98
                                                                                                                          20.99
                                                                                                                          87.8%
                                                                                                                          NA19107.assemble_contigs
                                                                                                                          9.3Kbp
                                                                                                                          4.8Kbp
                                                                                                                          85.6K
                                                                                                                          188.7K
                                                                                                                          111.4Kbp
                                                                                                                          2750.0Mbp
                                                                                                                          1799.0
                                                                                                                          110.58
                                                                                                                          24.62
                                                                                                                          89.0%
                                                                                                                          NA19118.assemble_contigs
                                                                                                                          8.4Kbp
                                                                                                                          4.3Kbp
                                                                                                                          93.3K
                                                                                                                          204.9K
                                                                                                                          127.5Kbp
                                                                                                                          2703.0Mbp
                                                                                                                          1549.0
                                                                                                                          107.68
                                                                                                                          20.82
                                                                                                                          87.8%
                                                                                                                          NA19129.assemble_contigs
                                                                                                                          10.8Kbp
                                                                                                                          5.6Kbp
                                                                                                                          73.9K
                                                                                                                          161.6K
                                                                                                                          123.6Kbp
                                                                                                                          2734.4Mbp
                                                                                                                          1892.0
                                                                                                                          111.13
                                                                                                                          24.89
                                                                                                                          88.7%
                                                                                                                          NA19131.assemble_contigs
                                                                                                                          12.0Kbp
                                                                                                                          6.2Kbp
                                                                                                                          66.2K
                                                                                                                          145.3K
                                                                                                                          133.7Kbp
                                                                                                                          2732.8Mbp
                                                                                                                          1801.0
                                                                                                                          111.39
                                                                                                                          25.10
                                                                                                                          88.7%
                                                                                                                          PAV0Q.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          3.5Kbp
                                                                                                                          116.2K
                                                                                                                          254.5K
                                                                                                                          86.9Kbp
                                                                                                                          2693.0Mbp
                                                                                                                          648.0
                                                                                                                          103.54
                                                                                                                          20.49
                                                                                                                          87.4%
                                                                                                                          PAZ0V.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          3.5Kbp
                                                                                                                          117.5K
                                                                                                                          256.3K
                                                                                                                          102.2Kbp
                                                                                                                          2677.5Mbp
                                                                                                                          592.0
                                                                                                                          103.41
                                                                                                                          20.20
                                                                                                                          86.9%
                                                                                                                          PBA0X.assemble_contigs
                                                                                                                          6.8Kbp
                                                                                                                          3.5Kbp
                                                                                                                          114.6K
                                                                                                                          251.1K
                                                                                                                          82.7Kbp
                                                                                                                          2692.6Mbp
                                                                                                                          635.0
                                                                                                                          103.68
                                                                                                                          20.49
                                                                                                                          87.4%
                                                                                                                          PBC0A.assemble_contigs
                                                                                                                          6.7Kbp
                                                                                                                          3.5Kbp
                                                                                                                          116.9K
                                                                                                                          255.1K
                                                                                                                          80.9Kbp
                                                                                                                          2677.5Mbp
                                                                                                                          572.0
                                                                                                                          103.63
                                                                                                                          20.27
                                                                                                                          86.9%
                                                                                                                          SAMEA2580885.assemble_contigs
                                                                                                                          4.9Kbp
                                                                                                                          2.5Kbp
                                                                                                                          161.9K
                                                                                                                          355.2K
                                                                                                                          63.0Kbp
                                                                                                                          2720.3Mbp
                                                                                                                          1826.0
                                                                                                                          108.65
                                                                                                                          20.14
                                                                                                                          87.7%
                                                                                                                          SAMEA2580886.assemble_contigs
                                                                                                                          5.8Kbp
                                                                                                                          3.0Kbp
                                                                                                                          135.7K
                                                                                                                          296.9K
                                                                                                                          83.8Kbp
                                                                                                                          2719.7Mbp
                                                                                                                          1736.0
                                                                                                                          108.34
                                                                                                                          20.19
                                                                                                                          88.0%
                                                                                                                          SAMEA2580889.assemble_contigs
                                                                                                                          5.8Kbp
                                                                                                                          3.0Kbp
                                                                                                                          135.4K
                                                                                                                          295.7K
                                                                                                                          87.6Kbp
                                                                                                                          2714.4Mbp
                                                                                                                          1714.0
                                                                                                                          107.94
                                                                                                                          19.88
                                                                                                                          87.9%
                                                                                                                          SAMEA2580891.assemble_contigs
                                                                                                                          5.9Kbp
                                                                                                                          3.1Kbp
                                                                                                                          133.3K
                                                                                                                          290.9K
                                                                                                                          74.3Kbp
                                                                                                                          2699.9Mbp
                                                                                                                          1598.0
                                                                                                                          108.18
                                                                                                                          19.95
                                                                                                                          87.4%
                                                                                                                          SAMEA2580897.assemble_contigs
                                                                                                                          7.9Kbp
                                                                                                                          4.0Kbp
                                                                                                                          98.5K
                                                                                                                          218.4K
                                                                                                                          109.4Kbp
                                                                                                                          2726.5Mbp
                                                                                                                          1412.0
                                                                                                                          107.25
                                                                                                                          24.01
                                                                                                                          88.1%
                                                                                                                          SAMEA3506075.assemble_contigs
                                                                                                                          10.1Kbp
                                                                                                                          5.2Kbp
                                                                                                                          78.2K
                                                                                                                          172.3K
                                                                                                                          122.5Kbp
                                                                                                                          2739.4Mbp
                                                                                                                          1470.0
                                                                                                                          108.36
                                                                                                                          24.30
                                                                                                                          88.8%
                                                                                                                          SAMEA3506076.assemble_contigs
                                                                                                                          10.8Kbp
                                                                                                                          5.5Kbp
                                                                                                                          72.7K
                                                                                                                          160.5K
                                                                                                                          130.5Kbp
                                                                                                                          2722.1Mbp
                                                                                                                          1406.0
                                                                                                                          108.36
                                                                                                                          24.36
                                                                                                                          88.3%
                                                                                                                          SAMEA3506077.assemble_contigs
                                                                                                                          9.2Kbp
                                                                                                                          4.7Kbp
                                                                                                                          86.3K
                                                                                                                          190.2K
                                                                                                                          108.3Kbp
                                                                                                                          2740.3Mbp
                                                                                                                          1478.0
                                                                                                                          108.28
                                                                                                                          24.19
                                                                                                                          88.8%
                                                                                                                          SAMEA3506078.assemble_contigs
                                                                                                                          7.6Kbp
                                                                                                                          3.9Kbp
                                                                                                                          102.9K
                                                                                                                          229.4K
                                                                                                                          111.6Kbp
                                                                                                                          2741.2Mbp
                                                                                                                          1423.0
                                                                                                                          107.91
                                                                                                                          23.84
                                                                                                                          88.6%
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                                                                                                                          - Number of Contigs - -

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                                                                                                                          This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                          BUSCO

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                                                                                                                          BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

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                                                                                                                          - Lineage: eukaryota_odb10 - -

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                                                                                                                          - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

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                                                                                                                                - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                - Bioinformatics (2016)
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                                                                                                                                About MultiQC

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                                                                                                                                This report was generated using MultiQC, version 1.12

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                                                                                                                                MultiQC is published in Bioinformatics:

                                                                                                                                -
                                                                                                                                - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                - Bioinformatics (2016)
                                                                                                                                - doi: 10.1093/bioinformatics/btw354
                                                                                                                                - PMID: 27312411 -
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                                                                                                                                - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                Report - - generated on 2022-02-15, 22:07 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/finalgenomeset/KhoeSan/logs/0a/72750879f1c2d26a267c2a2a456bc7

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                                                                                                                                General Statistics

                                                                                                                                - - - - - - - - - - - Showing 19/19 rows and 2/2 columns. - -
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                                                                                                                                Sample NameN50 (Kbp)Assembly Length (Mbp)
                                                                                                                                KSP062.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                2492.7Mbp
                                                                                                                                KSP065.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                2506.1Mbp
                                                                                                                                KSP069.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                2503.4Mbp
                                                                                                                                KSP092.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                2517.1Mbp
                                                                                                                                KSP096.assemble_contigs
                                                                                                                                1.7Kbp
                                                                                                                                2445.2Mbp
                                                                                                                                KSP103.assemble_contigs
                                                                                                                                1.8Kbp
                                                                                                                                2383.6Mbp
                                                                                                                                KSP106.assemble_contigs
                                                                                                                                2.1Kbp
                                                                                                                                2456.8Mbp
                                                                                                                                KSP116.assemble_contigs
                                                                                                                                2.5Kbp
                                                                                                                                2530.2Mbp
                                                                                                                                KSP134.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                2508.1Mbp
                                                                                                                                KSP137.assemble_contigs
                                                                                                                                2.0Kbp
                                                                                                                                2477.1Mbp
                                                                                                                                KSP139.assemble_contigs
                                                                                                                                2.6Kbp
                                                                                                                                2549.4Mbp
                                                                                                                                KSP140.assemble_contigs
                                                                                                                                2.4Kbp
                                                                                                                                2525.9Mbp
                                                                                                                                KSP146.assemble_contigs
                                                                                                                                2.5Kbp
                                                                                                                                2528.9Mbp
                                                                                                                                KSP152.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                2528.4Mbp
                                                                                                                                KSP155.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                2530.8Mbp
                                                                                                                                KSP224.assemble_contigs
                                                                                                                                2.4Kbp
                                                                                                                                2554.3Mbp
                                                                                                                                KSP228.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                2534.6Mbp
                                                                                                                                LP6005443_DNA_G08.assemble_contigs
                                                                                                                                1.2Kbp
                                                                                                                                2150.8Mbp
                                                                                                                                SAMEA2580840.assemble_contigs
                                                                                                                                5.2Kbp
                                                                                                                                2698.9Mbp
                                                                                                                                - - -
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                                                                                                                                -

                                                                                                                                QUAST

                                                                                                                                -

                                                                                                                                QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

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                                                                                                                                - Assembly Statistics - -

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                                                                                                                                - - - - - - - - - Showing 19/19 rows and 10/10 columns. - -
                                                                                                                                -
                                                                                                                                - -
                                                                                                                                Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                KSP062.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                1.2Kbp
                                                                                                                                320.5K
                                                                                                                                705.8K
                                                                                                                                39.5Kbp
                                                                                                                                2492.7Mbp
                                                                                                                                2376.0
                                                                                                                                108.32
                                                                                                                                17.11
                                                                                                                                79.9%
                                                                                                                                KSP065.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                1.2Kbp
                                                                                                                                316.2K
                                                                                                                                693.3K
                                                                                                                                46.7Kbp
                                                                                                                                2506.1Mbp
                                                                                                                                2587.0
                                                                                                                                106.93
                                                                                                                                17.04
                                                                                                                                80.3%
                                                                                                                                KSP069.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                1.2Kbp
                                                                                                                                309.7K
                                                                                                                                687.7K
                                                                                                                                42.5Kbp
                                                                                                                                2503.4Mbp
                                                                                                                                2061.0
                                                                                                                                108.16
                                                                                                                                17.27
                                                                                                                                80.3%
                                                                                                                                KSP092.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                1.2Kbp
                                                                                                                                316.3K
                                                                                                                                692.2K
                                                                                                                                39.0Kbp
                                                                                                                                2517.1Mbp
                                                                                                                                2560.0
                                                                                                                                107.87
                                                                                                                                17.37
                                                                                                                                80.7%
                                                                                                                                KSP096.assemble_contigs
                                                                                                                                1.7Kbp
                                                                                                                                1.0Kbp
                                                                                                                                419.9K
                                                                                                                                884.4K
                                                                                                                                26.8Kbp
                                                                                                                                2445.2Mbp
                                                                                                                                7358.0
                                                                                                                                106.03
                                                                                                                                17.17
                                                                                                                                78.0%
                                                                                                                                KSP103.assemble_contigs
                                                                                                                                1.8Kbp
                                                                                                                                1.1Kbp
                                                                                                                                383.6K
                                                                                                                                817.4K
                                                                                                                                25.9Kbp
                                                                                                                                2383.6Mbp
                                                                                                                                6297.0
                                                                                                                                108.18
                                                                                                                                17.43
                                                                                                                                76.1%
                                                                                                                                KSP106.assemble_contigs
                                                                                                                                2.1Kbp
                                                                                                                                1.2Kbp
                                                                                                                                335.5K
                                                                                                                                731.4K
                                                                                                                                32.0Kbp
                                                                                                                                2456.8Mbp
                                                                                                                                3772.0
                                                                                                                                109.42
                                                                                                                                17.17
                                                                                                                                78.7%
                                                                                                                                KSP116.assemble_contigs
                                                                                                                                2.5Kbp
                                                                                                                                1.3Kbp
                                                                                                                                279.9K
                                                                                                                                628.8K
                                                                                                                                59.0Kbp
                                                                                                                                2530.2Mbp
                                                                                                                                2030.0
                                                                                                                                110.40
                                                                                                                                17.36
                                                                                                                                81.3%
                                                                                                                                KSP134.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                1.2Kbp
                                                                                                                                318.1K
                                                                                                                                697.2K
                                                                                                                                40.7Kbp
                                                                                                                                2508.1Mbp
                                                                                                                                2803.0
                                                                                                                                105.88
                                                                                                                                16.68
                                                                                                                                80.4%
                                                                                                                                KSP137.assemble_contigs
                                                                                                                                2.0Kbp
                                                                                                                                1.1Kbp
                                                                                                                                351.4K
                                                                                                                                762.3K
                                                                                                                                41.3Kbp
                                                                                                                                2477.1Mbp
                                                                                                                                3703.0
                                                                                                                                104.93
                                                                                                                                16.79
                                                                                                                                79.3%
                                                                                                                                KSP139.assemble_contigs
                                                                                                                                2.6Kbp
                                                                                                                                1.4Kbp
                                                                                                                                270.6K
                                                                                                                                609.0K
                                                                                                                                49.9Kbp
                                                                                                                                2549.4Mbp
                                                                                                                                1908.0
                                                                                                                                107.40
                                                                                                                                17.14
                                                                                                                                82.0%
                                                                                                                                KSP140.assemble_contigs
                                                                                                                                2.4Kbp
                                                                                                                                1.3Kbp
                                                                                                                                290.7K
                                                                                                                                649.1K
                                                                                                                                44.7Kbp
                                                                                                                                2525.9Mbp
                                                                                                                                2058.0
                                                                                                                                106.49
                                                                                                                                16.81
                                                                                                                                81.1%
                                                                                                                                KSP146.assemble_contigs
                                                                                                                                2.5Kbp
                                                                                                                                1.3Kbp
                                                                                                                                283.6K
                                                                                                                                634.6K
                                                                                                                                48.4Kbp
                                                                                                                                2528.9Mbp
                                                                                                                                1879.0
                                                                                                                                107.57
                                                                                                                                16.96
                                                                                                                                81.3%
                                                                                                                                KSP152.assemble_contigs
                                                                                                                                2.2Kbp
                                                                                                                                1.2Kbp
                                                                                                                                324.0K
                                                                                                                                710.1K
                                                                                                                                38.7Kbp
                                                                                                                                2528.4Mbp
                                                                                                                                2808.0
                                                                                                                                107.26
                                                                                                                                17.24
                                                                                                                                81.0%
                                                                                                                                KSP155.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                1.3Kbp
                                                                                                                                310.8K
                                                                                                                                686.3K
                                                                                                                                41.8Kbp
                                                                                                                                2530.8Mbp
                                                                                                                                2475.0
                                                                                                                                107.36
                                                                                                                                17.29
                                                                                                                                81.1%
                                                                                                                                KSP224.assemble_contigs
                                                                                                                                2.4Kbp
                                                                                                                                1.3Kbp
                                                                                                                                300.7K
                                                                                                                                661.2K
                                                                                                                                63.9Kbp
                                                                                                                                2554.3Mbp
                                                                                                                                1794.0
                                                                                                                                108.13
                                                                                                                                17.27
                                                                                                                                81.9%
                                                                                                                                KSP228.assemble_contigs
                                                                                                                                2.3Kbp
                                                                                                                                1.2Kbp
                                                                                                                                316.0K
                                                                                                                                696.1K
                                                                                                                                46.1Kbp
                                                                                                                                2534.6Mbp
                                                                                                                                1965.0
                                                                                                                                106.59
                                                                                                                                17.39
                                                                                                                                81.2%
                                                                                                                                LP6005443_DNA_G08.assemble_contigs
                                                                                                                                1.2Kbp
                                                                                                                                0.8Kbp
                                                                                                                                535.2K
                                                                                                                                1076.7K
                                                                                                                                30.3Kbp
                                                                                                                                2150.8Mbp
                                                                                                                                1404.0
                                                                                                                                96.50
                                                                                                                                15.53
                                                                                                                                68.7%
                                                                                                                                SAMEA2580840.assemble_contigs
                                                                                                                                5.2Kbp
                                                                                                                                2.7Kbp
                                                                                                                                149.8K
                                                                                                                                327.1K
                                                                                                                                76.0Kbp
                                                                                                                                2698.9Mbp
                                                                                                                                1744.0
                                                                                                                                119.06
                                                                                                                                19.98
                                                                                                                                87.4%
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                                                                                                                                - Number of Contigs - -

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                                                                                                                                This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                                BUSCO

                                                                                                                                -

                                                                                                                                BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.DOI: 10.1093/bioinformatics/btv351.

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                                                                                                                                - Lineage: eukaryota_odb10 - -

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                                                                                                                                - - - - - MultiQC v1.12 - - - Written by Phil Ewels, - available on GitHub. -

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                                                                                                                                - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                                                      - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                      - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                      - Bioinformatics (2016)
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                                                                                                                                      About MultiQC

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                                                                                                                                      This report was generated using MultiQC, version 1.9

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                                                                                                                                      You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                                                      For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                                                                      You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

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                                                                                                                                      MultiQC is published in Bioinformatics:

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                                                                                                                                      - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                      - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                      - Bioinformatics (2016)
                                                                                                                                      - doi: 10.1093/bioinformatics/btw354
                                                                                                                                      - PMID: 27312411 -
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                                                                                                                                      - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                      Report - - generated on 2022-03-30, 11:19 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/BantuNC

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                                                                                                                                      General Statistics

                                                                                                                                      - - - - - - - - - - Showing 37/37 rows and 2/2 columns. - -
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                                                                                                                                      Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                      LP6005441_DNA_B02.assemble_contigs
                                                                                                                                      0.9Kbp
                                                                                                                                      1860.1Mbp
                                                                                                                                      LP6005441_DNA_F01.assemble_contigs
                                                                                                                                      1.1Kbp
                                                                                                                                      1957.2Mbp
                                                                                                                                      LP6005443_DNA_A01.assemble_contigs
                                                                                                                                      1.3Kbp
                                                                                                                                      2182.1Mbp
                                                                                                                                      LP6005443_DNA_E02.assemble_contigs
                                                                                                                                      1.2Kbp
                                                                                                                                      2111.6Mbp
                                                                                                                                      LP6005443_DNA_F02.assemble_contigs
                                                                                                                                      1.0Kbp
                                                                                                                                      1763.6Mbp
                                                                                                                                      LP6005443_DNA_G02.assemble_contigs
                                                                                                                                      1.1Kbp
                                                                                                                                      2006.5Mbp
                                                                                                                                      NA19028.assemble_contigs
                                                                                                                                      8.0Kbp
                                                                                                                                      2719.7Mbp
                                                                                                                                      NA19038.assemble_contigs
                                                                                                                                      8.2Kbp
                                                                                                                                      2703.8Mbp
                                                                                                                                      NA19309.assemble_contigs
                                                                                                                                      8.4Kbp
                                                                                                                                      2751.0Mbp
                                                                                                                                      NA19317.assemble_contigs
                                                                                                                                      8.4Kbp
                                                                                                                                      2721.0Mbp
                                                                                                                                      NA19318.assemble_contigs
                                                                                                                                      11.0Kbp
                                                                                                                                      2749.5Mbp
                                                                                                                                      NA19328.assemble_contigs
                                                                                                                                      12.3Kbp
                                                                                                                                      2729.4Mbp
                                                                                                                                      NA19332.assemble_contigs
                                                                                                                                      8.5Kbp
                                                                                                                                      2706.5Mbp
                                                                                                                                      NA19350.assemble_contigs
                                                                                                                                      7.8Kbp
                                                                                                                                      2720.1Mbp
                                                                                                                                      NA19372.assemble_contigs
                                                                                                                                      9.8Kbp
                                                                                                                                      2749.7Mbp
                                                                                                                                      NA19380.assemble_contigs
                                                                                                                                      7.9Kbp
                                                                                                                                      2719.0Mbp
                                                                                                                                      NA19385.assemble_contigs
                                                                                                                                      8.1Kbp
                                                                                                                                      2721.1Mbp
                                                                                                                                      NA19434.assemble_contigs
                                                                                                                                      9.9Kbp
                                                                                                                                      2732.8Mbp
                                                                                                                                      NA19448.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      2750.4Mbp
                                                                                                                                      NA19461.assemble_contigs
                                                                                                                                      9.8Kbp
                                                                                                                                      2751.1Mbp
                                                                                                                                      NA19463.assemble_contigs
                                                                                                                                      8.2Kbp
                                                                                                                                      2708.0Mbp
                                                                                                                                      NA19467.assemble_contigs
                                                                                                                                      9.7Kbp
                                                                                                                                      2736.1Mbp
                                                                                                                                      NA19471.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      2737.2Mbp
                                                                                                                                      NA19473.assemble_contigs
                                                                                                                                      9.2Kbp
                                                                                                                                      2737.4Mbp
                                                                                                                                      SAMEA2580844.assemble_contigs
                                                                                                                                      6.1Kbp
                                                                                                                                      2716.4Mbp
                                                                                                                                      SAMEA2580845.assemble_contigs
                                                                                                                                      5.6Kbp
                                                                                                                                      2709.8Mbp
                                                                                                                                      SAMEA2580848.assemble_contigs
                                                                                                                                      5.8Kbp
                                                                                                                                      2712.7Mbp
                                                                                                                                      SAMEA2580849.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      2730.6Mbp
                                                                                                                                      SAMEA2580852.assemble_contigs
                                                                                                                                      5.8Kbp
                                                                                                                                      2712.1Mbp
                                                                                                                                      SAMEA2580853.assemble_contigs
                                                                                                                                      5.7Kbp
                                                                                                                                      2712.8Mbp
                                                                                                                                      SAMEA2580854.assemble_contigs
                                                                                                                                      5.9Kbp
                                                                                                                                      2713.3Mbp
                                                                                                                                      SAMEA2580855.assemble_contigs
                                                                                                                                      6.0Kbp
                                                                                                                                      2715.6Mbp
                                                                                                                                      SAMEA2580856.assemble_contigs
                                                                                                                                      5.7Kbp
                                                                                                                                      2716.2Mbp
                                                                                                                                      SAMEA2580858.assemble_contigs
                                                                                                                                      2.0Kbp
                                                                                                                                      2522.0Mbp
                                                                                                                                      SAMEA2580859.assemble_contigs
                                                                                                                                      3.9Kbp
                                                                                                                                      2691.3Mbp
                                                                                                                                      SAMEA2580861.assemble_contigs
                                                                                                                                      2.1Kbp
                                                                                                                                      2548.3Mbp
                                                                                                                                      SAMEA2580862.assemble_contigs
                                                                                                                                      2.0Kbp
                                                                                                                                      2506.8Mbp
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                                                                                                                                      QUAST

                                                                                                                                      -

                                                                                                                                      QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

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                                                                                                                                      - Assembly Statistics - -

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                                                                                                                                      - - - - - - - - - Showing 37/37 rows and 10/10 columns. - -
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                                                                                                                                      Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                      LP6005441_DNA_B02.assemble_contigs
                                                                                                                                      0.9Kbp
                                                                                                                                      0.7Kbp
                                                                                                                                      674.3K
                                                                                                                                      1259607.0K
                                                                                                                                      12.1Kbp
                                                                                                                                      1860.1Mbp
                                                                                                                                      965.0
                                                                                                                                      77.74
                                                                                                                                      12.11
                                                                                                                                      59.4%
                                                                                                                                      LP6005441_DNA_F01.assemble_contigs
                                                                                                                                      1.1Kbp
                                                                                                                                      0.7Kbp
                                                                                                                                      600.4K
                                                                                                                                      1159419.0K
                                                                                                                                      11.9Kbp
                                                                                                                                      1957.2Mbp
                                                                                                                                      1030.0
                                                                                                                                      82.73
                                                                                                                                      13.15
                                                                                                                                      62.5%
                                                                                                                                      LP6005443_DNA_A01.assemble_contigs
                                                                                                                                      1.3Kbp
                                                                                                                                      0.8Kbp
                                                                                                                                      512.1K
                                                                                                                                      1043404.0K
                                                                                                                                      20.6Kbp
                                                                                                                                      2182.1Mbp
                                                                                                                                      1279.0
                                                                                                                                      85.30
                                                                                                                                      13.89
                                                                                                                                      69.7%
                                                                                                                                      LP6005443_DNA_E02.assemble_contigs
                                                                                                                                      1.2Kbp
                                                                                                                                      0.8Kbp
                                                                                                                                      544.7K
                                                                                                                                      1088768.0K
                                                                                                                                      23.9Kbp
                                                                                                                                      2111.6Mbp
                                                                                                                                      1209.0
                                                                                                                                      85.25
                                                                                                                                      14.03
                                                                                                                                      67.4%
                                                                                                                                      LP6005443_DNA_F02.assemble_contigs
                                                                                                                                      1.0Kbp
                                                                                                                                      0.7Kbp
                                                                                                                                      611.2K
                                                                                                                                      1155130.0K
                                                                                                                                      27.8Kbp
                                                                                                                                      1763.6Mbp
                                                                                                                                      817.0
                                                                                                                                      80.13
                                                                                                                                      12.66
                                                                                                                                      56.4%
                                                                                                                                      LP6005443_DNA_G02.assemble_contigs
                                                                                                                                      1.1Kbp
                                                                                                                                      0.8Kbp
                                                                                                                                      570.5K
                                                                                                                                      1120871.0K
                                                                                                                                      16.6Kbp
                                                                                                                                      2006.5Mbp
                                                                                                                                      973.0
                                                                                                                                      85.70
                                                                                                                                      13.81
                                                                                                                                      64.1%
                                                                                                                                      NA19028.assemble_contigs
                                                                                                                                      8.0Kbp
                                                                                                                                      4.1Kbp
                                                                                                                                      97.7K
                                                                                                                                      214795.0K
                                                                                                                                      113.8Kbp
                                                                                                                                      2719.7Mbp
                                                                                                                                      1547.0
                                                                                                                                      107.83
                                                                                                                                      21.03
                                                                                                                                      88.3%
                                                                                                                                      NA19038.assemble_contigs
                                                                                                                                      8.2Kbp
                                                                                                                                      4.2Kbp
                                                                                                                                      95.3K
                                                                                                                                      209954.0K
                                                                                                                                      118.3Kbp
                                                                                                                                      2703.8Mbp
                                                                                                                                      1474.0
                                                                                                                                      107.51
                                                                                                                                      21.06
                                                                                                                                      87.8%
                                                                                                                                      NA19309.assemble_contigs
                                                                                                                                      8.4Kbp
                                                                                                                                      4.3Kbp
                                                                                                                                      93.7K
                                                                                                                                      206766.0K
                                                                                                                                      115.6Kbp
                                                                                                                                      2751.0Mbp
                                                                                                                                      1912.0
                                                                                                                                      110.33
                                                                                                                                      24.37
                                                                                                                                      89.0%
                                                                                                                                      NA19317.assemble_contigs
                                                                                                                                      8.4Kbp
                                                                                                                                      4.3Kbp
                                                                                                                                      93.0K
                                                                                                                                      205026.0K
                                                                                                                                      106.1Kbp
                                                                                                                                      2721.0Mbp
                                                                                                                                      1600.0
                                                                                                                                      107.81
                                                                                                                                      21.14
                                                                                                                                      88.4%
                                                                                                                                      NA19318.assemble_contigs
                                                                                                                                      11.0Kbp
                                                                                                                                      5.7Kbp
                                                                                                                                      73.0K
                                                                                                                                      159601.0K
                                                                                                                                      129.2Kbp
                                                                                                                                      2749.5Mbp
                                                                                                                                      1901.0
                                                                                                                                      110.76
                                                                                                                                      25.07
                                                                                                                                      89.2%
                                                                                                                                      NA19328.assemble_contigs
                                                                                                                                      12.3Kbp
                                                                                                                                      6.3Kbp
                                                                                                                                      64.3K
                                                                                                                                      141222.0K
                                                                                                                                      143.3Kbp
                                                                                                                                      2729.4Mbp
                                                                                                                                      1833.0
                                                                                                                                      111.62
                                                                                                                                      24.98
                                                                                                                                      88.6%
                                                                                                                                      NA19332.assemble_contigs
                                                                                                                                      8.5Kbp
                                                                                                                                      4.4Kbp
                                                                                                                                      92.4K
                                                                                                                                      203310.0K
                                                                                                                                      102.1Kbp
                                                                                                                                      2706.5Mbp
                                                                                                                                      1610.0
                                                                                                                                      107.74
                                                                                                                                      21.15
                                                                                                                                      87.9%
                                                                                                                                      NA19350.assemble_contigs
                                                                                                                                      7.8Kbp
                                                                                                                                      4.0Kbp
                                                                                                                                      100.2K
                                                                                                                                      220742.0K
                                                                                                                                      95.2Kbp
                                                                                                                                      2720.1Mbp
                                                                                                                                      1580.0
                                                                                                                                      107.41
                                                                                                                                      21.03
                                                                                                                                      88.3%
                                                                                                                                      NA19372.assemble_contigs
                                                                                                                                      9.8Kbp
                                                                                                                                      5.0Kbp
                                                                                                                                      81.2K
                                                                                                                                      178868.0K
                                                                                                                                      151.6Kbp
                                                                                                                                      2749.7Mbp
                                                                                                                                      1896.0
                                                                                                                                      111.22
                                                                                                                                      24.84
                                                                                                                                      89.1%
                                                                                                                                      NA19380.assemble_contigs
                                                                                                                                      7.9Kbp
                                                                                                                                      4.1Kbp
                                                                                                                                      99.1K
                                                                                                                                      218008.0K
                                                                                                                                      100.3Kbp
                                                                                                                                      2719.0Mbp
                                                                                                                                      1522.0
                                                                                                                                      107.32
                                                                                                                                      21.02
                                                                                                                                      88.2%
                                                                                                                                      NA19385.assemble_contigs
                                                                                                                                      8.1Kbp
                                                                                                                                      4.2Kbp
                                                                                                                                      97.0K
                                                                                                                                      213510.0K
                                                                                                                                      129.6Kbp
                                                                                                                                      2721.1Mbp
                                                                                                                                      1571.0
                                                                                                                                      107.94
                                                                                                                                      21.15
                                                                                                                                      88.3%
                                                                                                                                      NA19434.assemble_contigs
                                                                                                                                      9.9Kbp
                                                                                                                                      5.1Kbp
                                                                                                                                      80.3K
                                                                                                                                      176521.0K
                                                                                                                                      118.9Kbp
                                                                                                                                      2732.8Mbp
                                                                                                                                      1785.0
                                                                                                                                      109.77
                                                                                                                                      24.53
                                                                                                                                      88.5%
                                                                                                                                      NA19448.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      4.9Kbp
                                                                                                                                      83.2K
                                                                                                                                      183640.0K
                                                                                                                                      132.2Kbp
                                                                                                                                      2750.4Mbp
                                                                                                                                      1947.0
                                                                                                                                      111.19
                                                                                                                                      24.72
                                                                                                                                      89.1%
                                                                                                                                      NA19461.assemble_contigs
                                                                                                                                      9.8Kbp
                                                                                                                                      5.1Kbp
                                                                                                                                      81.5K
                                                                                                                                      178733.0K
                                                                                                                                      114.8Kbp
                                                                                                                                      2751.1Mbp
                                                                                                                                      1891.0
                                                                                                                                      110.49
                                                                                                                                      24.73
                                                                                                                                      89.1%
                                                                                                                                      NA19463.assemble_contigs
                                                                                                                                      8.2Kbp
                                                                                                                                      4.2Kbp
                                                                                                                                      95.9K
                                                                                                                                      210657.0K
                                                                                                                                      158.2Kbp
                                                                                                                                      2708.0Mbp
                                                                                                                                      1628.0
                                                                                                                                      108.24
                                                                                                                                      21.00
                                                                                                                                      87.9%
                                                                                                                                      NA19467.assemble_contigs
                                                                                                                                      9.7Kbp
                                                                                                                                      5.0Kbp
                                                                                                                                      81.3K
                                                                                                                                      178658.0K
                                                                                                                                      134.5Kbp
                                                                                                                                      2736.1Mbp
                                                                                                                                      1958.0
                                                                                                                                      110.66
                                                                                                                                      24.60
                                                                                                                                      88.6%
                                                                                                                                      NA19471.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      4.9Kbp
                                                                                                                                      84.1K
                                                                                                                                      183944.0K
                                                                                                                                      120.4Kbp
                                                                                                                                      2737.2Mbp
                                                                                                                                      1952.0
                                                                                                                                      111.47
                                                                                                                                      24.82
                                                                                                                                      88.6%
                                                                                                                                      NA19473.assemble_contigs
                                                                                                                                      9.2Kbp
                                                                                                                                      4.8Kbp
                                                                                                                                      86.0K
                                                                                                                                      188147.0K
                                                                                                                                      121.2Kbp
                                                                                                                                      2737.4Mbp
                                                                                                                                      1836.0
                                                                                                                                      110.59
                                                                                                                                      24.72
                                                                                                                                      88.6%
                                                                                                                                      SAMEA2580844.assemble_contigs
                                                                                                                                      6.1Kbp
                                                                                                                                      3.2Kbp
                                                                                                                                      130.0K
                                                                                                                                      283516.0K
                                                                                                                                      79.3Kbp
                                                                                                                                      2716.4Mbp
                                                                                                                                      1575.0
                                                                                                                                      111.19
                                                                                                                                      20.63
                                                                                                                                      87.9%
                                                                                                                                      SAMEA2580845.assemble_contigs
                                                                                                                                      5.6Kbp
                                                                                                                                      2.9Kbp
                                                                                                                                      141.3K
                                                                                                                                      308562.0K
                                                                                                                                      72.4Kbp
                                                                                                                                      2709.8Mbp
                                                                                                                                      1613.0
                                                                                                                                      110.68
                                                                                                                                      19.81
                                                                                                                                      87.7%
                                                                                                                                      SAMEA2580848.assemble_contigs
                                                                                                                                      5.8Kbp
                                                                                                                                      3.0Kbp
                                                                                                                                      136.1K
                                                                                                                                      297496.0K
                                                                                                                                      83.7Kbp
                                                                                                                                      2712.7Mbp
                                                                                                                                      1670.0
                                                                                                                                      109.22
                                                                                                                                      19.60
                                                                                                                                      87.8%
                                                                                                                                      SAMEA2580849.assemble_contigs
                                                                                                                                      9.5Kbp
                                                                                                                                      4.8Kbp
                                                                                                                                      82.6K
                                                                                                                                      183386.0K
                                                                                                                                      118.6Kbp
                                                                                                                                      2730.6Mbp
                                                                                                                                      1491.0
                                                                                                                                      110.00
                                                                                                                                      24.33
                                                                                                                                      88.4%
                                                                                                                                      SAMEA2580852.assemble_contigs
                                                                                                                                      5.8Kbp
                                                                                                                                      3.0Kbp
                                                                                                                                      135.9K
                                                                                                                                      296651.0K
                                                                                                                                      81.3Kbp
                                                                                                                                      2712.1Mbp
                                                                                                                                      1581.0
                                                                                                                                      108.18
                                                                                                                                      19.49
                                                                                                                                      87.8%
                                                                                                                                      SAMEA2580853.assemble_contigs
                                                                                                                                      5.7Kbp
                                                                                                                                      3.0Kbp
                                                                                                                                      138.4K
                                                                                                                                      302010.0K
                                                                                                                                      76.7Kbp
                                                                                                                                      2712.8Mbp
                                                                                                                                      1632.0
                                                                                                                                      108.50
                                                                                                                                      19.47
                                                                                                                                      87.8%
                                                                                                                                      SAMEA2580854.assemble_contigs
                                                                                                                                      5.9Kbp
                                                                                                                                      3.1Kbp
                                                                                                                                      134.3K
                                                                                                                                      293539.0K
                                                                                                                                      82.7Kbp
                                                                                                                                      2713.3Mbp
                                                                                                                                      1702.0
                                                                                                                                      108.29
                                                                                                                                      19.58
                                                                                                                                      87.9%
                                                                                                                                      SAMEA2580855.assemble_contigs
                                                                                                                                      6.0Kbp
                                                                                                                                      3.1Kbp
                                                                                                                                      132.4K
                                                                                                                                      288842.0K
                                                                                                                                      74.6Kbp
                                                                                                                                      2715.6Mbp
                                                                                                                                      1694.0
                                                                                                                                      107.96
                                                                                                                                      19.53
                                                                                                                                      87.9%
                                                                                                                                      SAMEA2580856.assemble_contigs
                                                                                                                                      5.7Kbp
                                                                                                                                      3.0Kbp
                                                                                                                                      137.9K
                                                                                                                                      302013.0K
                                                                                                                                      74.1Kbp
                                                                                                                                      2716.2Mbp
                                                                                                                                      1613.0
                                                                                                                                      107.93
                                                                                                                                      19.73
                                                                                                                                      87.9%
                                                                                                                                      SAMEA2580858.assemble_contigs
                                                                                                                                      2.0Kbp
                                                                                                                                      1.1Kbp
                                                                                                                                      372.8K
                                                                                                                                      791736.0K
                                                                                                                                      35.8Kbp
                                                                                                                                      2522.0Mbp
                                                                                                                                      1391.0
                                                                                                                                      103.45
                                                                                                                                      15.93
                                                                                                                                      80.4%
                                                                                                                                      SAMEA2580859.assemble_contigs
                                                                                                                                      3.9Kbp
                                                                                                                                      2.0Kbp
                                                                                                                                      200.2K
                                                                                                                                      439279.0K
                                                                                                                                      73.7Kbp
                                                                                                                                      2691.3Mbp
                                                                                                                                      1697.0
                                                                                                                                      105.49
                                                                                                                                      18.13
                                                                                                                                      86.6%
                                                                                                                                      SAMEA2580861.assemble_contigs
                                                                                                                                      2.1Kbp
                                                                                                                                      1.2Kbp
                                                                                                                                      353.1K
                                                                                                                                      752569.0K
                                                                                                                                      29.3Kbp
                                                                                                                                      2548.3Mbp
                                                                                                                                      1435.0
                                                                                                                                      104.40
                                                                                                                                      15.76
                                                                                                                                      81.4%
                                                                                                                                      SAMEA2580862.assemble_contigs
                                                                                                                                      2.0Kbp
                                                                                                                                      1.1Kbp
                                                                                                                                      375.1K
                                                                                                                                      795956.0K
                                                                                                                                      36.7Kbp
                                                                                                                                      2506.8Mbp
                                                                                                                                      1423.0
                                                                                                                                      104.43
                                                                                                                                      15.59
                                                                                                                                      80.0%
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                                                                                                                                      - Number of Contigs - -

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                                                                                                                                      This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                                      BUSCO

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                                                                                                                                      BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

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                                                                                                                                      - Lineage: eukaryota_odb10 - -

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                                                                                                                                      - - - - - MultiQC v1.9 - - - Written by Phil Ewels, - available on GitHub. -

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                                                                                                                                            - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                            - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
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                                                                                                                                            About MultiQC

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                                                                                                                                            This report was generated using MultiQC, version 1.11

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                                                                                                                                            MultiQC is published in Bioinformatics:

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                                                                                                                                            - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                            - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                            - Bioinformatics (2016)
                                                                                                                                            - doi: 10.1093/bioinformatics/btw354
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                                                                                                                                            - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                            Report - - generated on 2021-07-08, 10:42 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/intermediate/4d/0c63f3334396ed94ac2240f2cd1ca9

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                                                                                                                                            General Statistics

                                                                                                                                            - - - - - - - - - - - Showing 26/26 rows and 2/2 columns. - -
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                                                                                                                                            Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                            LP6005441_DNA_A08.assemble_contigs
                                                                                                                                            1.0Kbp
                                                                                                                                            1775.3Mbp
                                                                                                                                            LP6005441_DNA_B08.assemble_contigs
                                                                                                                                            0.9Kbp
                                                                                                                                            1767.6Mbp
                                                                                                                                            LP6005441_DNA_G02.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            2060.9Mbp
                                                                                                                                            LP6005441_DNA_H02.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            2057.6Mbp
                                                                                                                                            LP6005592_DNA_C03.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            1963.4Mbp
                                                                                                                                            SAMEA2580802.assemble_contigs
                                                                                                                                            3.9Kbp
                                                                                                                                            2697.1Mbp
                                                                                                                                            SAMEA2580803.assemble_contigs
                                                                                                                                            5.9Kbp
                                                                                                                                            2713.1Mbp
                                                                                                                                            SAMEA2580807.assemble_contigs
                                                                                                                                            5.9Kbp
                                                                                                                                            2712.8Mbp
                                                                                                                                            SAMEA2580808.assemble_contigs
                                                                                                                                            2.3Kbp
                                                                                                                                            2603.7Mbp
                                                                                                                                            SAMEA2580809.assemble_contigs
                                                                                                                                            9.2Kbp
                                                                                                                                            2737.4Mbp
                                                                                                                                            SAMEA2580813.assemble_contigs
                                                                                                                                            5.7Kbp
                                                                                                                                            2713.8Mbp
                                                                                                                                            SAMEA2580814.assemble_contigs
                                                                                                                                            5.3Kbp
                                                                                                                                            2684.3Mbp
                                                                                                                                            SAMEA2580815.assemble_contigs
                                                                                                                                            4.3Kbp
                                                                                                                                            2703.7Mbp
                                                                                                                                            SAMEA2580816.assemble_contigs
                                                                                                                                            5.1Kbp
                                                                                                                                            2688.7Mbp
                                                                                                                                            SAMEA2580818.assemble_contigs
                                                                                                                                            5.6Kbp
                                                                                                                                            2684.2Mbp
                                                                                                                                            SAMEA2580819.assemble_contigs
                                                                                                                                            5.5Kbp
                                                                                                                                            2688.3Mbp
                                                                                                                                            SAMEA2580820.assemble_contigs
                                                                                                                                            5.4Kbp
                                                                                                                                            2688.1Mbp
                                                                                                                                            SAMEA2580821.assemble_contigs
                                                                                                                                            3.5Kbp
                                                                                                                                            2692.6Mbp
                                                                                                                                            SAMEA2580822.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            2704.2Mbp
                                                                                                                                            SAMEA2580823.assemble_contigs
                                                                                                                                            5.0Kbp
                                                                                                                                            2703.5Mbp
                                                                                                                                            SAMEA2580830.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            2704.0Mbp
                                                                                                                                            SAMEA2580831.assemble_contigs
                                                                                                                                            6.0Kbp
                                                                                                                                            2699.3Mbp
                                                                                                                                            SAMEA2580834.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            2703.3Mbp
                                                                                                                                            SAMEA2580836.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            2703.9Mbp
                                                                                                                                            SAMEA3506072.assemble_contigs
                                                                                                                                            9.2Kbp
                                                                                                                                            2737.7Mbp
                                                                                                                                            SAMEA3506073.assemble_contigs
                                                                                                                                            10.2Kbp
                                                                                                                                            2738.9Mbp
                                                                                                                                            - - -
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                                                                                                                                            -

                                                                                                                                            QUAST

                                                                                                                                            -

                                                                                                                                            QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

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                                                                                                                                            - Assembly Statistics - -

                                                                                                                                            - - - - -
                                                                                                                                            - - - - - - - - - Showing 26/26 rows and 10/10 columns. - -
                                                                                                                                            -
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                                                                                                                                            Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                            LP6005441_DNA_A08.assemble_contigs
                                                                                                                                            1.0Kbp
                                                                                                                                            0.7Kbp
                                                                                                                                            615.0K
                                                                                                                                            1163.5K
                                                                                                                                            17.2Kbp
                                                                                                                                            1775.3Mbp
                                                                                                                                            841.0
                                                                                                                                            87.50
                                                                                                                                            13.84
                                                                                                                                            56.8%
                                                                                                                                            LP6005441_DNA_B08.assemble_contigs
                                                                                                                                            0.9Kbp
                                                                                                                                            0.7Kbp
                                                                                                                                            655.9K
                                                                                                                                            1221.5K
                                                                                                                                            12.8Kbp
                                                                                                                                            1767.6Mbp
                                                                                                                                            762.0
                                                                                                                                            85.27
                                                                                                                                            13.48
                                                                                                                                            56.5%
                                                                                                                                            LP6005441_DNA_G02.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            0.8Kbp
                                                                                                                                            573.5K
                                                                                                                                            1127.4K
                                                                                                                                            13.0Kbp
                                                                                                                                            2060.9Mbp
                                                                                                                                            1144.0
                                                                                                                                            88.07
                                                                                                                                            14.19
                                                                                                                                            65.8%
                                                                                                                                            LP6005441_DNA_H02.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            0.8Kbp
                                                                                                                                            577.3K
                                                                                                                                            1133.2K
                                                                                                                                            17.3Kbp
                                                                                                                                            2057.6Mbp
                                                                                                                                            1198.0
                                                                                                                                            88.37
                                                                                                                                            14.18
                                                                                                                                            65.7%
                                                                                                                                            LP6005592_DNA_C03.assemble_contigs
                                                                                                                                            1.1Kbp
                                                                                                                                            0.7Kbp
                                                                                                                                            594.5K
                                                                                                                                            1150.1K
                                                                                                                                            12.9Kbp
                                                                                                                                            1963.4Mbp
                                                                                                                                            1052.0
                                                                                                                                            90.42
                                                                                                                                            14.00
                                                                                                                                            62.7%
                                                                                                                                            SAMEA2580802.assemble_contigs
                                                                                                                                            3.9Kbp
                                                                                                                                            2.1Kbp
                                                                                                                                            196.9K
                                                                                                                                            432.3K
                                                                                                                                            55.3Kbp
                                                                                                                                            2697.1Mbp
                                                                                                                                            1728.0
                                                                                                                                            113.06
                                                                                                                                            19.97
                                                                                                                                            86.7%
                                                                                                                                            SAMEA2580803.assemble_contigs
                                                                                                                                            5.9Kbp
                                                                                                                                            3.1Kbp
                                                                                                                                            134.9K
                                                                                                                                            294.0K
                                                                                                                                            63.9Kbp
                                                                                                                                            2713.1Mbp
                                                                                                                                            1728.0
                                                                                                                                            114.73
                                                                                                                                            20.86
                                                                                                                                            87.8%
                                                                                                                                            SAMEA2580807.assemble_contigs
                                                                                                                                            5.9Kbp
                                                                                                                                            3.1Kbp
                                                                                                                                            133.6K
                                                                                                                                            291.5K
                                                                                                                                            66.8Kbp
                                                                                                                                            2712.8Mbp
                                                                                                                                            1877.0
                                                                                                                                            114.54
                                                                                                                                            20.80
                                                                                                                                            87.8%
                                                                                                                                            SAMEA2580808.assemble_contigs
                                                                                                                                            2.3Kbp
                                                                                                                                            1.3Kbp
                                                                                                                                            330.3K
                                                                                                                                            708.9K
                                                                                                                                            46.3Kbp
                                                                                                                                            2603.7Mbp
                                                                                                                                            1594.0
                                                                                                                                            110.86
                                                                                                                                            18.01
                                                                                                                                            83.0%
                                                                                                                                            SAMEA2580809.assemble_contigs
                                                                                                                                            9.2Kbp
                                                                                                                                            4.7Kbp
                                                                                                                                            86.2K
                                                                                                                                            189.8K
                                                                                                                                            124.1Kbp
                                                                                                                                            2737.4Mbp
                                                                                                                                            1414.0
                                                                                                                                            113.70
                                                                                                                                            25.59
                                                                                                                                            88.6%
                                                                                                                                            SAMEA2580813.assemble_contigs
                                                                                                                                            5.7Kbp
                                                                                                                                            3.0Kbp
                                                                                                                                            139.3K
                                                                                                                                            303.6K
                                                                                                                                            60.5Kbp
                                                                                                                                            2713.8Mbp
                                                                                                                                            1793.0
                                                                                                                                            114.39
                                                                                                                                            20.69
                                                                                                                                            87.8%
                                                                                                                                            SAMEA2580814.assemble_contigs
                                                                                                                                            5.3Kbp
                                                                                                                                            2.8Kbp
                                                                                                                                            147.1K
                                                                                                                                            322.1K
                                                                                                                                            60.2Kbp
                                                                                                                                            2684.3Mbp
                                                                                                                                            1685.0
                                                                                                                                            110.83
                                                                                                                                            17.10
                                                                                                                                            87.0%
                                                                                                                                            SAMEA2580815.assemble_contigs
                                                                                                                                            4.3Kbp
                                                                                                                                            2.3Kbp
                                                                                                                                            182.9K
                                                                                                                                            399.0K
                                                                                                                                            53.6Kbp
                                                                                                                                            2703.7Mbp
                                                                                                                                            1770.0
                                                                                                                                            113.14
                                                                                                                                            20.02
                                                                                                                                            87.1%
                                                                                                                                            SAMEA2580816.assemble_contigs
                                                                                                                                            5.1Kbp
                                                                                                                                            2.7Kbp
                                                                                                                                            152.8K
                                                                                                                                            333.2K
                                                                                                                                            62.1Kbp
                                                                                                                                            2688.7Mbp
                                                                                                                                            1699.0
                                                                                                                                            112.17
                                                                                                                                            18.37
                                                                                                                                            87.0%
                                                                                                                                            SAMEA2580818.assemble_contigs
                                                                                                                                            5.6Kbp
                                                                                                                                            2.9Kbp
                                                                                                                                            140.3K
                                                                                                                                            306.5K
                                                                                                                                            79.1Kbp
                                                                                                                                            2684.2Mbp
                                                                                                                                            1547.0
                                                                                                                                            111.63
                                                                                                                                            18.19
                                                                                                                                            87.0%
                                                                                                                                            SAMEA2580819.assemble_contigs
                                                                                                                                            5.5Kbp
                                                                                                                                            2.9Kbp
                                                                                                                                            140.9K
                                                                                                                                            308.1K
                                                                                                                                            69.7Kbp
                                                                                                                                            2688.3Mbp
                                                                                                                                            1656.0
                                                                                                                                            113.09
                                                                                                                                            18.59
                                                                                                                                            87.1%
                                                                                                                                            SAMEA2580820.assemble_contigs
                                                                                                                                            5.4Kbp
                                                                                                                                            2.8Kbp
                                                                                                                                            143.9K
                                                                                                                                            314.4K
                                                                                                                                            64.1Kbp
                                                                                                                                            2688.1Mbp
                                                                                                                                            1567.0
                                                                                                                                            112.72
                                                                                                                                            18.42
                                                                                                                                            87.1%
                                                                                                                                            SAMEA2580821.assemble_contigs
                                                                                                                                            3.5Kbp
                                                                                                                                            1.9Kbp
                                                                                                                                            218.6K
                                                                                                                                            478.2K
                                                                                                                                            65.1Kbp
                                                                                                                                            2692.6Mbp
                                                                                                                                            1615.0
                                                                                                                                            112.56
                                                                                                                                            19.92
                                                                                                                                            86.4%
                                                                                                                                            SAMEA2580822.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            3.0Kbp
                                                                                                                                            136.6K
                                                                                                                                            298.3K
                                                                                                                                            73.7Kbp
                                                                                                                                            2704.2Mbp
                                                                                                                                            1685.0
                                                                                                                                            113.64
                                                                                                                                            19.52
                                                                                                                                            87.6%
                                                                                                                                            SAMEA2580823.assemble_contigs
                                                                                                                                            5.0Kbp
                                                                                                                                            2.6Kbp
                                                                                                                                            159.0K
                                                                                                                                            346.5K
                                                                                                                                            60.7Kbp
                                                                                                                                            2703.5Mbp
                                                                                                                                            1731.0
                                                                                                                                            113.67
                                                                                                                                            20.10
                                                                                                                                            87.3%
                                                                                                                                            SAMEA2580830.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            3.0Kbp
                                                                                                                                            135.8K
                                                                                                                                            296.6K
                                                                                                                                            68.4Kbp
                                                                                                                                            2704.0Mbp
                                                                                                                                            1681.0
                                                                                                                                            115.61
                                                                                                                                            19.82
                                                                                                                                            87.6%
                                                                                                                                            SAMEA2580831.assemble_contigs
                                                                                                                                            6.0Kbp
                                                                                                                                            3.1Kbp
                                                                                                                                            130.5K
                                                                                                                                            284.7K
                                                                                                                                            69.9Kbp
                                                                                                                                            2699.3Mbp
                                                                                                                                            1641.0
                                                                                                                                            116.42
                                                                                                                                            21.34
                                                                                                                                            87.4%
                                                                                                                                            SAMEA2580834.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            3.0Kbp
                                                                                                                                            135.5K
                                                                                                                                            296.0K
                                                                                                                                            61.8Kbp
                                                                                                                                            2703.3Mbp
                                                                                                                                            1675.0
                                                                                                                                            115.94
                                                                                                                                            19.81
                                                                                                                                            87.6%
                                                                                                                                            SAMEA2580836.assemble_contigs
                                                                                                                                            5.8Kbp
                                                                                                                                            3.0Kbp
                                                                                                                                            135.6K
                                                                                                                                            296.2K
                                                                                                                                            66.3Kbp
                                                                                                                                            2703.9Mbp
                                                                                                                                            1723.0
                                                                                                                                            115.54
                                                                                                                                            19.78
                                                                                                                                            87.6%
                                                                                                                                            SAMEA3506072.assemble_contigs
                                                                                                                                            9.2Kbp
                                                                                                                                            4.7Kbp
                                                                                                                                            85.7K
                                                                                                                                            188.9K
                                                                                                                                            109.5Kbp
                                                                                                                                            2737.7Mbp
                                                                                                                                            1518.0
                                                                                                                                            114.24
                                                                                                                                            25.36
                                                                                                                                            88.7%
                                                                                                                                            SAMEA3506073.assemble_contigs
                                                                                                                                            10.2Kbp
                                                                                                                                            5.2Kbp
                                                                                                                                            78.0K
                                                                                                                                            172.0K
                                                                                                                                            126.3Kbp
                                                                                                                                            2738.9Mbp
                                                                                                                                            1607.0
                                                                                                                                            115.45
                                                                                                                                            25.72
                                                                                                                                            88.8%
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                                                                                                                                            - Number of Contigs - -

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                                                                                                                                            This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                                                  - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                  - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                  - Bioinformatics (2016)
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                                                                                                                                                  About MultiQC

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                                                                                                                                                  This report was generated using MultiQC, version 1.9

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                                                                                                                                                  MultiQC is published in Bioinformatics:

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                                                                                                                                                  - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                  - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                  - Bioinformatics (2016)
                                                                                                                                                  - doi: 10.1093/bioinformatics/btw354
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                                                                                                                                                  - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                                  Report - - generated on 2022-03-30, 10:49 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/CWNC

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                                                                                                                                                  General Statistics

                                                                                                                                                  - - - - - - - - - - Showing 54/54 rows and 2/2 columns. - -
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                                                                                                                                                  - -
                                                                                                                                                  Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                                  10_150304_L001.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  1904.1Mbp
                                                                                                                                                  11_150302_L002.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1584.3Mbp
                                                                                                                                                  12_150304_L004.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  1945.6Mbp
                                                                                                                                                  13_RB103T_C_150611_L007.assemble_contigs
                                                                                                                                                  1.3Kbp
                                                                                                                                                  2097.9Mbp
                                                                                                                                                  14_150304_L001.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1839.8Mbp
                                                                                                                                                  16_RB106T_C_150611_L008.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1709.8Mbp
                                                                                                                                                  17_150304_L002.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  1812.4Mbp
                                                                                                                                                  18_RB108T_C_150611_L008.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  1872.0Mbp
                                                                                                                                                  20_150302_L001.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  1519.5Mbp
                                                                                                                                                  22_150304_L004.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  1984.1Mbp
                                                                                                                                                  24_RB114T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  265.1Mbp
                                                                                                                                                  24_RB114T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  300.6Mbp
                                                                                                                                                  25_RB115T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  239.3Mbp
                                                                                                                                                  25_RB115T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  270.3Mbp
                                                                                                                                                  26_RB116T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  1326.3Mbp
                                                                                                                                                  26_RB116T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  1395.1Mbp
                                                                                                                                                  27_150304_L003.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  1879.0Mbp
                                                                                                                                                  28_RB118T_C_150616_L003.assemble_contigs
                                                                                                                                                  1.4Kbp
                                                                                                                                                  2010.9Mbp
                                                                                                                                                  29_RB119T_C_150616_L003.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  1320.9Mbp
                                                                                                                                                  30_RB122T_C_150616_L004.assemble_contigs
                                                                                                                                                  1.4Kbp
                                                                                                                                                  2049.0Mbp
                                                                                                                                                  31_150304_L003.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1720.9Mbp
                                                                                                                                                  32_RB124T_C_150616_L004.assemble_contigs
                                                                                                                                                  0.8Kbp
                                                                                                                                                  630.2Mbp
                                                                                                                                                  37_RB142T_C_150616_L005.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1510.5Mbp
                                                                                                                                                  38_RB151T_C_150616_L005.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  1821.4Mbp
                                                                                                                                                  39_150304_L002.assemble_contigs
                                                                                                                                                  1.3Kbp
                                                                                                                                                  1916.0Mbp
                                                                                                                                                  4_RB091T_C_150611_L006.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1747.5Mbp
                                                                                                                                                  5_150302_L001.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1718.1Mbp
                                                                                                                                                  6_150302_L002.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1549.2Mbp
                                                                                                                                                  7_RB094T_C_150611_L006.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  1715.7Mbp
                                                                                                                                                  CB12.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  2693.0Mbp
                                                                                                                                                  CB14.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  2674.9Mbp
                                                                                                                                                  CB15.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  2692.6Mbp
                                                                                                                                                  CB16.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  2689.1Mbp
                                                                                                                                                  CB17.assemble_contigs
                                                                                                                                                  4.9Kbp
                                                                                                                                                  2699.5Mbp
                                                                                                                                                  CB24.assemble_contigs
                                                                                                                                                  6.6Kbp
                                                                                                                                                  2692.1Mbp
                                                                                                                                                  CB29.assemble_contigs
                                                                                                                                                  5.3Kbp
                                                                                                                                                  2698.7Mbp
                                                                                                                                                  CB31.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  2690.9Mbp
                                                                                                                                                  CB32.assemble_contigs
                                                                                                                                                  5.4Kbp
                                                                                                                                                  2682.4Mbp
                                                                                                                                                  CB33.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  2676.9Mbp
                                                                                                                                                  CB7.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  2677.7Mbp
                                                                                                                                                  CF24.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  2689.1Mbp
                                                                                                                                                  CF25.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  2689.5Mbp
                                                                                                                                                  CF26.assemble_contigs
                                                                                                                                                  6.2Kbp
                                                                                                                                                  2680.6Mbp
                                                                                                                                                  CF27.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  2692.9Mbp
                                                                                                                                                  CF30.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  2691.1Mbp
                                                                                                                                                  CF37.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  2688.5Mbp
                                                                                                                                                  CF46.assemble_contigs
                                                                                                                                                  6.2Kbp
                                                                                                                                                  2671.4Mbp
                                                                                                                                                  CF49.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  2673.5Mbp
                                                                                                                                                  CP17.assemble_contigs
                                                                                                                                                  6.0Kbp
                                                                                                                                                  2672.2Mbp
                                                                                                                                                  CP28.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  2691.5Mbp
                                                                                                                                                  CP36.assemble_contigs
                                                                                                                                                  5.8Kbp
                                                                                                                                                  2679.1Mbp
                                                                                                                                                  CP38.assemble_contigs
                                                                                                                                                  5.9Kbp
                                                                                                                                                  2679.4Mbp
                                                                                                                                                  CP40.assemble_contigs
                                                                                                                                                  5.4Kbp
                                                                                                                                                  2698.9Mbp
                                                                                                                                                  CP48.assemble_contigs
                                                                                                                                                  5.9Kbp
                                                                                                                                                  2679.7Mbp
                                                                                                                                                  - - -
                                                                                                                                                  - - - - - - -
                                                                                                                                                  -

                                                                                                                                                  QUAST

                                                                                                                                                  -

                                                                                                                                                  QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                                                                                                                                  - - - - -
                                                                                                                                                  - -

                                                                                                                                                  - Assembly Statistics - -

                                                                                                                                                  - - - - -
                                                                                                                                                  - - - - - - - - - Showing 54/54 rows and 10/10 columns. - -
                                                                                                                                                  -
                                                                                                                                                  - -
                                                                                                                                                  Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                                  10_150304_L001.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  509.6K
                                                                                                                                                  1006234.0K
                                                                                                                                                  24.2Kbp
                                                                                                                                                  1904.1Mbp
                                                                                                                                                  1511.0
                                                                                                                                                  99.85
                                                                                                                                                  14.72
                                                                                                                                                  61.4%
                                                                                                                                                  11_150302_L002.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  524.3K
                                                                                                                                                  998095.0K
                                                                                                                                                  11.7Kbp
                                                                                                                                                  1584.3Mbp
                                                                                                                                                  1228.0
                                                                                                                                                  93.49
                                                                                                                                                  12.66
                                                                                                                                                  51.3%
                                                                                                                                                  12_150304_L004.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  517.9K
                                                                                                                                                  1023760.0K
                                                                                                                                                  14.5Kbp
                                                                                                                                                  1945.6Mbp
                                                                                                                                                  1439.0
                                                                                                                                                  96.38
                                                                                                                                                  14.00
                                                                                                                                                  62.7%
                                                                                                                                                  13_RB103T_C_150611_L007.assemble_contigs
                                                                                                                                                  1.3Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  485.4K
                                                                                                                                                  982253.0K
                                                                                                                                                  19.0Kbp
                                                                                                                                                  2097.9Mbp
                                                                                                                                                  1652.0
                                                                                                                                                  99.54
                                                                                                                                                  14.24
                                                                                                                                                  67.4%
                                                                                                                                                  14_150304_L001.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  587.9K
                                                                                                                                                  1116876.0K
                                                                                                                                                  18.1Kbp
                                                                                                                                                  1839.8Mbp
                                                                                                                                                  1559.0
                                                                                                                                                  95.43
                                                                                                                                                  13.70
                                                                                                                                                  59.4%
                                                                                                                                                  16_RB106T_C_150611_L008.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  540.4K
                                                                                                                                                  1032609.0K
                                                                                                                                                  12.0Kbp
                                                                                                                                                  1709.8Mbp
                                                                                                                                                  1406.0
                                                                                                                                                  96.26
                                                                                                                                                  13.08
                                                                                                                                                  55.3%
                                                                                                                                                  17_150304_L002.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  546.7K
                                                                                                                                                  1054633.0K
                                                                                                                                                  17.1Kbp
                                                                                                                                                  1812.4Mbp
                                                                                                                                                  1402.0
                                                                                                                                                  94.77
                                                                                                                                                  13.78
                                                                                                                                                  58.5%
                                                                                                                                                  18_RB108T_C_150611_L008.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  535.4K
                                                                                                                                                  1045600.0K
                                                                                                                                                  12.8Kbp
                                                                                                                                                  1872.0Mbp
                                                                                                                                                  1518.0
                                                                                                                                                  95.63
                                                                                                                                                  13.90
                                                                                                                                                  60.4%
                                                                                                                                                  20_150302_L001.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  558.0K
                                                                                                                                                  1037670.0K
                                                                                                                                                  11.2Kbp
                                                                                                                                                  1519.5Mbp
                                                                                                                                                  1230.0
                                                                                                                                                  92.93
                                                                                                                                                  12.68
                                                                                                                                                  49.3%
                                                                                                                                                  22_150304_L004.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  500.2K
                                                                                                                                                  997127.0K
                                                                                                                                                  15.7Kbp
                                                                                                                                                  1984.1Mbp
                                                                                                                                                  1465.0
                                                                                                                                                  98.21
                                                                                                                                                  14.35
                                                                                                                                                  63.9%
                                                                                                                                                  24_RB114T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  0.6Kbp
                                                                                                                                                  164.6K
                                                                                                                                                  276029.0K
                                                                                                                                                  8.6Kbp
                                                                                                                                                  265.1Mbp
                                                                                                                                                  404.0
                                                                                                                                                  97.28
                                                                                                                                                  9.98
                                                                                                                                                  8.7%
                                                                                                                                                  24_RB114T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  0.6Kbp
                                                                                                                                                  183.7K
                                                                                                                                                  308956.0K
                                                                                                                                                  9.2Kbp
                                                                                                                                                  300.6Mbp
                                                                                                                                                  470.0
                                                                                                                                                  96.14
                                                                                                                                                  10.12
                                                                                                                                                  9.8%
                                                                                                                                                  25_RB115T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  0.6Kbp
                                                                                                                                                  149.3K
                                                                                                                                                  250120.0K
                                                                                                                                                  8.9Kbp
                                                                                                                                                  239.3Mbp
                                                                                                                                                  375.0
                                                                                                                                                  93.32
                                                                                                                                                  10.08
                                                                                                                                                  7.8%
                                                                                                                                                  25_RB115T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.6Kbp
                                                                                                                                                  0.6Kbp
                                                                                                                                                  165.9K
                                                                                                                                                  278903.0K
                                                                                                                                                  6.5Kbp
                                                                                                                                                  270.3Mbp
                                                                                                                                                  378.0
                                                                                                                                                  92.22
                                                                                                                                                  9.99
                                                                                                                                                  8.8%
                                                                                                                                                  26_RB116T_C_150616_L001.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  518.1K
                                                                                                                                                  957300.0K
                                                                                                                                                  10.3Kbp
                                                                                                                                                  1326.3Mbp
                                                                                                                                                  1205.0
                                                                                                                                                  93.48
                                                                                                                                                  12.60
                                                                                                                                                  43.1%
                                                                                                                                                  26_RB116T_C_150616_L002.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  525.6K
                                                                                                                                                  978108.0K
                                                                                                                                                  11.4Kbp
                                                                                                                                                  1395.1Mbp
                                                                                                                                                  1292.0
                                                                                                                                                  93.94
                                                                                                                                                  12.63
                                                                                                                                                  45.3%
                                                                                                                                                  27_150304_L003.assemble_contigs
                                                                                                                                                  1.1Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  560.6K
                                                                                                                                                  1081855.0K
                                                                                                                                                  14.5Kbp
                                                                                                                                                  1879.0Mbp
                                                                                                                                                  1506.0
                                                                                                                                                  95.02
                                                                                                                                                  13.83
                                                                                                                                                  60.7%
                                                                                                                                                  28_RB118T_C_150616_L003.assemble_contigs
                                                                                                                                                  1.4Kbp
                                                                                                                                                  0.9Kbp
                                                                                                                                                  434.6K
                                                                                                                                                  895124.0K
                                                                                                                                                  22.1Kbp
                                                                                                                                                  2010.9Mbp
                                                                                                                                                  1559.0
                                                                                                                                                  97.41
                                                                                                                                                  14.07
                                                                                                                                                  64.6%
                                                                                                                                                  29_RB119T_C_150616_L003.assemble_contigs
                                                                                                                                                  0.9Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  501.0K
                                                                                                                                                  924986.0K
                                                                                                                                                  12.2Kbp
                                                                                                                                                  1320.9Mbp
                                                                                                                                                  1049.0
                                                                                                                                                  93.74
                                                                                                                                                  12.44
                                                                                                                                                  42.9%
                                                                                                                                                  30_RB122T_C_150616_L004.assemble_contigs
                                                                                                                                                  1.4Kbp
                                                                                                                                                  0.9Kbp
                                                                                                                                                  419.1K
                                                                                                                                                  876680.0K
                                                                                                                                                  23.3Kbp
                                                                                                                                                  2049.0Mbp
                                                                                                                                                  1490.0
                                                                                                                                                  99.56
                                                                                                                                                  14.46
                                                                                                                                                  65.8%
                                                                                                                                                  31_150304_L003.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  547.5K
                                                                                                                                                  1043436.0K
                                                                                                                                                  12.4Kbp
                                                                                                                                                  1720.9Mbp
                                                                                                                                                  1326.0
                                                                                                                                                  96.01
                                                                                                                                                  13.61
                                                                                                                                                  55.6%
                                                                                                                                                  32_RB124T_C_150616_L004.assemble_contigs
                                                                                                                                                  0.8Kbp
                                                                                                                                                  0.6Kbp
                                                                                                                                                  307.3K
                                                                                                                                                  541613.0K
                                                                                                                                                  7.1Kbp
                                                                                                                                                  630.2Mbp
                                                                                                                                                  647.0
                                                                                                                                                  91.57
                                                                                                                                                  11.61
                                                                                                                                                  20.5%
                                                                                                                                                  37_RB142T_C_150616_L005.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  472.4K
                                                                                                                                                  909069.0K
                                                                                                                                                  11.9Kbp
                                                                                                                                                  1510.5Mbp
                                                                                                                                                  1218.0
                                                                                                                                                  92.53
                                                                                                                                                  12.57
                                                                                                                                                  48.8%
                                                                                                                                                  38_RB151T_C_150616_L005.assemble_contigs
                                                                                                                                                  1.2Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  485.5K
                                                                                                                                                  965089.0K
                                                                                                                                                  15.8Kbp
                                                                                                                                                  1821.4Mbp
                                                                                                                                                  1423.0
                                                                                                                                                  96.79
                                                                                                                                                  12.91
                                                                                                                                                  58.8%
                                                                                                                                                  39_150304_L002.assemble_contigs
                                                                                                                                                  1.3Kbp
                                                                                                                                                  0.8Kbp
                                                                                                                                                  468.8K
                                                                                                                                                  948459.0K
                                                                                                                                                  21.3Kbp
                                                                                                                                                  1916.0Mbp
                                                                                                                                                  1350.0
                                                                                                                                                  95.97
                                                                                                                                                  14.24
                                                                                                                                                  61.7%
                                                                                                                                                  4_RB091T_C_150611_L006.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  582.8K
                                                                                                                                                  1101317.0K
                                                                                                                                                  14.8Kbp
                                                                                                                                                  1747.5Mbp
                                                                                                                                                  1509.0
                                                                                                                                                  94.64
                                                                                                                                                  13.21
                                                                                                                                                  56.5%
                                                                                                                                                  5_150302_L001.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  546.2K
                                                                                                                                                  1044576.0K
                                                                                                                                                  13.4Kbp
                                                                                                                                                  1718.1Mbp
                                                                                                                                                  1373.0
                                                                                                                                                  94.55
                                                                                                                                                  13.17
                                                                                                                                                  55.5%
                                                                                                                                                  6_150302_L002.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  488.2K
                                                                                                                                                  938525.0K
                                                                                                                                                  27.6Kbp
                                                                                                                                                  1549.2Mbp
                                                                                                                                                  1213.0
                                                                                                                                                  97.44
                                                                                                                                                  12.30
                                                                                                                                                  50.1%
                                                                                                                                                  7_RB094T_C_150611_L006.assemble_contigs
                                                                                                                                                  1.0Kbp
                                                                                                                                                  0.7Kbp
                                                                                                                                                  534.8K
                                                                                                                                                  1028528.0K
                                                                                                                                                  12.6Kbp
                                                                                                                                                  1715.7Mbp
                                                                                                                                                  1413.0
                                                                                                                                                  96.21
                                                                                                                                                  13.79
                                                                                                                                                  55.4%
                                                                                                                                                  CB12.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  3.5Kbp
                                                                                                                                                  117.4K
                                                                                                                                                  256974.0K
                                                                                                                                                  75.6Kbp
                                                                                                                                                  2693.0Mbp
                                                                                                                                                  591.0
                                                                                                                                                  104.75
                                                                                                                                                  20.62
                                                                                                                                                  87.4%
                                                                                                                                                  CB14.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  121.2K
                                                                                                                                                  264667.0K
                                                                                                                                                  64.8Kbp
                                                                                                                                                  2674.9Mbp
                                                                                                                                                  553.0
                                                                                                                                                  104.47
                                                                                                                                                  20.19
                                                                                                                                                  86.8%
                                                                                                                                                  CB15.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  120.4K
                                                                                                                                                  263809.0K
                                                                                                                                                  101.2Kbp
                                                                                                                                                  2692.6Mbp
                                                                                                                                                  628.0
                                                                                                                                                  105.01
                                                                                                                                                  20.66
                                                                                                                                                  87.3%
                                                                                                                                                  CB16.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  123.2K
                                                                                                                                                  270417.0K
                                                                                                                                                  72.7Kbp
                                                                                                                                                  2689.1Mbp
                                                                                                                                                  587.0
                                                                                                                                                  104.23
                                                                                                                                                  20.25
                                                                                                                                                  87.2%
                                                                                                                                                  CB17.assemble_contigs
                                                                                                                                                  4.9Kbp
                                                                                                                                                  2.6Kbp
                                                                                                                                                  162.5K
                                                                                                                                                  351948.0K
                                                                                                                                                  71.4Kbp
                                                                                                                                                  2699.5Mbp
                                                                                                                                                  725.0
                                                                                                                                                  105.12
                                                                                                                                                  20.73
                                                                                                                                                  87.0%
                                                                                                                                                  CB24.assemble_contigs
                                                                                                                                                  6.6Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  118.0K
                                                                                                                                                  258410.0K
                                                                                                                                                  74.9Kbp
                                                                                                                                                  2692.1Mbp
                                                                                                                                                  693.0
                                                                                                                                                  104.59
                                                                                                                                                  20.33
                                                                                                                                                  87.3%
                                                                                                                                                  CB29.assemble_contigs
                                                                                                                                                  5.3Kbp
                                                                                                                                                  2.8Kbp
                                                                                                                                                  148.4K
                                                                                                                                                  322099.0K
                                                                                                                                                  65.4Kbp
                                                                                                                                                  2698.7Mbp
                                                                                                                                                  648.0
                                                                                                                                                  104.36
                                                                                                                                                  20.31
                                                                                                                                                  87.1%
                                                                                                                                                  CB31.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  119.7K
                                                                                                                                                  262297.0K
                                                                                                                                                  77.5Kbp
                                                                                                                                                  2690.9Mbp
                                                                                                                                                  625.0
                                                                                                                                                  104.44
                                                                                                                                                  20.30
                                                                                                                                                  87.3%
                                                                                                                                                  CB32.assemble_contigs
                                                                                                                                                  5.4Kbp
                                                                                                                                                  2.9Kbp
                                                                                                                                                  145.1K
                                                                                                                                                  315052.0K
                                                                                                                                                  78.1Kbp
                                                                                                                                                  2682.4Mbp
                                                                                                                                                  686.0
                                                                                                                                                  104.88
                                                                                                                                                  20.46
                                                                                                                                                  86.7%
                                                                                                                                                  CB33.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  120.9K
                                                                                                                                                  264336.0K
                                                                                                                                                  68.5Kbp
                                                                                                                                                  2676.9Mbp
                                                                                                                                                  611.0
                                                                                                                                                  104.70
                                                                                                                                                  20.27
                                                                                                                                                  86.8%
                                                                                                                                                  CB7.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  123.0K
                                                                                                                                                  268438.0K
                                                                                                                                                  76.2Kbp
                                                                                                                                                  2677.7Mbp
                                                                                                                                                  607.0
                                                                                                                                                  104.89
                                                                                                                                                  20.30
                                                                                                                                                  86.8%
                                                                                                                                                  CF24.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  121.0K
                                                                                                                                                  265419.0K
                                                                                                                                                  78.7Kbp
                                                                                                                                                  2689.1Mbp
                                                                                                                                                  613.0
                                                                                                                                                  104.11
                                                                                                                                                  20.29
                                                                                                                                                  87.2%
                                                                                                                                                  CF25.assemble_contigs
                                                                                                                                                  6.4Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  121.6K
                                                                                                                                                  267194.0K
                                                                                                                                                  80.5Kbp
                                                                                                                                                  2689.5Mbp
                                                                                                                                                  594.0
                                                                                                                                                  103.85
                                                                                                                                                  20.40
                                                                                                                                                  87.2%
                                                                                                                                                  CF26.assemble_contigs
                                                                                                                                                  6.2Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  125.2K
                                                                                                                                                  273508.0K
                                                                                                                                                  68.5Kbp
                                                                                                                                                  2680.6Mbp
                                                                                                                                                  707.0
                                                                                                                                                  104.61
                                                                                                                                                  20.40
                                                                                                                                                  86.9%
                                                                                                                                                  CF27.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  124.8K
                                                                                                                                                  272860.0K
                                                                                                                                                  82.5Kbp
                                                                                                                                                  2692.9Mbp
                                                                                                                                                  679.0
                                                                                                                                                  104.41
                                                                                                                                                  20.39
                                                                                                                                                  87.3%
                                                                                                                                                  CF30.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  3.5Kbp
                                                                                                                                                  117.2K
                                                                                                                                                  256576.0K
                                                                                                                                                  70.5Kbp
                                                                                                                                                  2691.1Mbp
                                                                                                                                                  608.0
                                                                                                                                                  103.95
                                                                                                                                                  20.40
                                                                                                                                                  87.3%
                                                                                                                                                  CF37.assemble_contigs
                                                                                                                                                  6.5Kbp
                                                                                                                                                  3.4Kbp
                                                                                                                                                  119.5K
                                                                                                                                                  262693.0K
                                                                                                                                                  76.4Kbp
                                                                                                                                                  2688.5Mbp
                                                                                                                                                  590.0
                                                                                                                                                  103.79
                                                                                                                                                  20.26
                                                                                                                                                  87.2%
                                                                                                                                                  CF46.assemble_contigs
                                                                                                                                                  6.2Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  124.6K
                                                                                                                                                  272103.0K
                                                                                                                                                  75.1Kbp
                                                                                                                                                  2671.4Mbp
                                                                                                                                                  675.0
                                                                                                                                                  104.22
                                                                                                                                                  20.06
                                                                                                                                                  86.6%
                                                                                                                                                  CF49.assemble_contigs
                                                                                                                                                  6.3Kbp
                                                                                                                                                  3.3Kbp
                                                                                                                                                  124.5K
                                                                                                                                                  272252.0K
                                                                                                                                                  74.3Kbp
                                                                                                                                                  2673.5Mbp
                                                                                                                                                  599.0
                                                                                                                                                  103.89
                                                                                                                                                  20.06
                                                                                                                                                  86.7%
                                                                                                                                                  CP17.assemble_contigs
                                                                                                                                                  6.0Kbp
                                                                                                                                                  3.1Kbp
                                                                                                                                                  129.4K
                                                                                                                                                  283668.0K
                                                                                                                                                  67.2Kbp
                                                                                                                                                  2672.2Mbp
                                                                                                                                                  670.0
                                                                                                                                                  103.99
                                                                                                                                                  20.23
                                                                                                                                                  86.6%
                                                                                                                                                  CP28.assemble_contigs
                                                                                                                                                  6.7Kbp
                                                                                                                                                  3.5Kbp
                                                                                                                                                  116.8K
                                                                                                                                                  256117.0K
                                                                                                                                                  82.6Kbp
                                                                                                                                                  2691.5Mbp
                                                                                                                                                  601.0
                                                                                                                                                  104.29
                                                                                                                                                  20.40
                                                                                                                                                  87.3%
                                                                                                                                                  CP36.assemble_contigs
                                                                                                                                                  5.8Kbp
                                                                                                                                                  3.1Kbp
                                                                                                                                                  135.2K
                                                                                                                                                  293793.0K
                                                                                                                                                  60.7Kbp
                                                                                                                                                  2679.1Mbp
                                                                                                                                                  673.0
                                                                                                                                                  104.08
                                                                                                                                                  20.14
                                                                                                                                                  86.7%
                                                                                                                                                  CP38.assemble_contigs
                                                                                                                                                  5.9Kbp
                                                                                                                                                  3.1Kbp
                                                                                                                                                  132.0K
                                                                                                                                                  287627.0K
                                                                                                                                                  82.4Kbp
                                                                                                                                                  2679.4Mbp
                                                                                                                                                  627.0
                                                                                                                                                  104.19
                                                                                                                                                  20.17
                                                                                                                                                  86.8%
                                                                                                                                                  CP40.assemble_contigs
                                                                                                                                                  5.4Kbp
                                                                                                                                                  2.9Kbp
                                                                                                                                                  146.4K
                                                                                                                                                  317450.0K
                                                                                                                                                  61.1Kbp
                                                                                                                                                  2698.9Mbp
                                                                                                                                                  707.0
                                                                                                                                                  104.61
                                                                                                                                                  20.50
                                                                                                                                                  87.2%
                                                                                                                                                  CP48.assemble_contigs
                                                                                                                                                  5.9Kbp
                                                                                                                                                  3.1Kbp
                                                                                                                                                  133.2K
                                                                                                                                                  290184.0K
                                                                                                                                                  71.0Kbp
                                                                                                                                                  2679.7Mbp
                                                                                                                                                  616.0
                                                                                                                                                  104.68
                                                                                                                                                  20.37
                                                                                                                                                  86.7%
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                                                                                                                                                  - Number of Contigs - -

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                                                                                                                                                  This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                                                  BUSCO

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                                                                                                                                                  BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

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                                                                                                                                                        - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                        - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                        - Bioinformatics (2016)
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                                                                                                                                                        About MultiQC

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                                                                                                                                                        This report was generated using MultiQC, version 1.9

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                                                                                                                                                        You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                                                                        For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                                                                                        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

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                                                                                                                                                        MultiQC is published in Bioinformatics:

                                                                                                                                                        -
                                                                                                                                                        - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                        - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                        - Bioinformatics (2016)
                                                                                                                                                        - doi: 10.1093/bioinformatics/btw354
                                                                                                                                                        - PMID: 27312411 -
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                                                                                                                                                        - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                                        Report - - generated on 2022-03-30, 11:10 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/EAAA

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                                                                                                                                                        General Statistics

                                                                                                                                                        - - - - - - - - - - Showing 29/29 rows and 2/2 columns. - -
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                                                                                                                                                        Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                                        LP6005442_DNA_D09.assemble_contigs
                                                                                                                                                        1.1Kbp
                                                                                                                                                        2101.9Mbp
                                                                                                                                                        egpg5305762.assemble_contigs
                                                                                                                                                        1.7Kbp
                                                                                                                                                        2016.7Mbp
                                                                                                                                                        egpg5305763.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        451.1Mbp
                                                                                                                                                        egpg5305765.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        533.7Mbp
                                                                                                                                                        egpg5305770.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        214.3Mbp
                                                                                                                                                        egpg5305771.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        181.3Mbp
                                                                                                                                                        egpg5305773.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        140.1Mbp
                                                                                                                                                        egpg5305778.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        577.4Mbp
                                                                                                                                                        egpg5305781.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        405.2Mbp
                                                                                                                                                        egpg5305904.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        612.4Mbp
                                                                                                                                                        egpg5305910.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        459.5Mbp
                                                                                                                                                        egpg5305911.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        602.1Mbp
                                                                                                                                                        egpg5305918.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        478.6Mbp
                                                                                                                                                        egpg5305919.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        401.9Mbp
                                                                                                                                                        egpg5305920.assemble_contigs
                                                                                                                                                        1.3Kbp
                                                                                                                                                        2070.7Mbp
                                                                                                                                                        egpg5305936.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        451.7Mbp
                                                                                                                                                        egpg5305937.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        652.4Mbp
                                                                                                                                                        egpg5305944.assemble_contigs
                                                                                                                                                        0.8Kbp
                                                                                                                                                        634.0Mbp
                                                                                                                                                        egpg5305945.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        622.2Mbp
                                                                                                                                                        egpg5305949.assemble_contigs
                                                                                                                                                        1.3Kbp
                                                                                                                                                        2036.2Mbp
                                                                                                                                                        egpg5305952.assemble_contigs
                                                                                                                                                        0.8Kbp
                                                                                                                                                        792.3Mbp
                                                                                                                                                        egpg5305953.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        627.3Mbp
                                                                                                                                                        egpg5305959.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        364.6Mbp
                                                                                                                                                        egpg5305960.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        317.2Mbp
                                                                                                                                                        egpg5305961.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        521.3Mbp
                                                                                                                                                        egpg5305967.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        440.7Mbp
                                                                                                                                                        egpg5305968.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        362.6Mbp
                                                                                                                                                        egpg5305969.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        317.6Mbp
                                                                                                                                                        egpg5305974.assemble_contigs
                                                                                                                                                        1.5Kbp
                                                                                                                                                        2292.4Mbp
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                                                                                                                                                        QUAST

                                                                                                                                                        -

                                                                                                                                                        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

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                                                                                                                                                        - Assembly Statistics - -

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                                                                                                                                                        - - - - - - - - - Showing 29/29 rows and 10/10 columns. - -
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                                                                                                                                                        Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                                        LP6005442_DNA_D09.assemble_contigs
                                                                                                                                                        1.1Kbp
                                                                                                                                                        0.8Kbp
                                                                                                                                                        597.4K
                                                                                                                                                        1169285.0K
                                                                                                                                                        12.6Kbp
                                                                                                                                                        2101.9Mbp
                                                                                                                                                        1063.0
                                                                                                                                                        77.87
                                                                                                                                                        12.51
                                                                                                                                                        67.1%
                                                                                                                                                        egpg5305762.assemble_contigs
                                                                                                                                                        1.7Kbp
                                                                                                                                                        1.0Kbp
                                                                                                                                                        359.1K
                                                                                                                                                        753908.0K
                                                                                                                                                        30.8Kbp
                                                                                                                                                        2016.7Mbp
                                                                                                                                                        1504.0
                                                                                                                                                        91.17
                                                                                                                                                        13.97
                                                                                                                                                        64.8%
                                                                                                                                                        egpg5305763.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        259.5K
                                                                                                                                                        442401.0K
                                                                                                                                                        9.5Kbp
                                                                                                                                                        451.1Mbp
                                                                                                                                                        334.0
                                                                                                                                                        77.17
                                                                                                                                                        8.50
                                                                                                                                                        14.7%
                                                                                                                                                        egpg5305765.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        292.0K
                                                                                                                                                        503146.0K
                                                                                                                                                        11.9Kbp
                                                                                                                                                        533.7Mbp
                                                                                                                                                        319.0
                                                                                                                                                        75.30
                                                                                                                                                        8.87
                                                                                                                                                        17.4%
                                                                                                                                                        egpg5305770.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        135.3K
                                                                                                                                                        226067.0K
                                                                                                                                                        6.4Kbp
                                                                                                                                                        214.3Mbp
                                                                                                                                                        229.0
                                                                                                                                                        78.48
                                                                                                                                                        8.44
                                                                                                                                                        7.0%
                                                                                                                                                        egpg5305771.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        118.3K
                                                                                                                                                        196280.0K
                                                                                                                                                        5.1Kbp
                                                                                                                                                        181.3Mbp
                                                                                                                                                        177.0
                                                                                                                                                        78.91
                                                                                                                                                        8.64
                                                                                                                                                        5.9%
                                                                                                                                                        egpg5305773.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        90.1K
                                                                                                                                                        149798.0K
                                                                                                                                                        4.5Kbp
                                                                                                                                                        140.1Mbp
                                                                                                                                                        126.0
                                                                                                                                                        74.60
                                                                                                                                                        9.30
                                                                                                                                                        4.6%
                                                                                                                                                        egpg5305778.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        317.5K
                                                                                                                                                        546442.0K
                                                                                                                                                        10.3Kbp
                                                                                                                                                        577.4Mbp
                                                                                                                                                        359.0
                                                                                                                                                        74.57
                                                                                                                                                        9.16
                                                                                                                                                        18.8%
                                                                                                                                                        egpg5305781.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        225.0K
                                                                                                                                                        386231.0K
                                                                                                                                                        4.6Kbp
                                                                                                                                                        405.2Mbp
                                                                                                                                                        227.0
                                                                                                                                                        75.14
                                                                                                                                                        9.53
                                                                                                                                                        13.2%
                                                                                                                                                        egpg5305904.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        330.5K
                                                                                                                                                        570137.0K
                                                                                                                                                        8.7Kbp
                                                                                                                                                        612.4Mbp
                                                                                                                                                        369.0
                                                                                                                                                        73.75
                                                                                                                                                        8.60
                                                                                                                                                        19.9%
                                                                                                                                                        egpg5305910.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        266.1K
                                                                                                                                                        452703.0K
                                                                                                                                                        6.3Kbp
                                                                                                                                                        459.5Mbp
                                                                                                                                                        332.0
                                                                                                                                                        74.23
                                                                                                                                                        8.40
                                                                                                                                                        15.0%
                                                                                                                                                        egpg5305911.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        329.6K
                                                                                                                                                        567203.0K
                                                                                                                                                        11.3Kbp
                                                                                                                                                        602.1Mbp
                                                                                                                                                        385.0
                                                                                                                                                        76.52
                                                                                                                                                        8.77
                                                                                                                                                        19.6%
                                                                                                                                                        egpg5305918.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        277.3K
                                                                                                                                                        471234.0K
                                                                                                                                                        5.4Kbp
                                                                                                                                                        478.6Mbp
                                                                                                                                                        275.0
                                                                                                                                                        74.67
                                                                                                                                                        8.66
                                                                                                                                                        15.6%
                                                                                                                                                        egpg5305919.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        241.9K
                                                                                                                                                        407736.0K
                                                                                                                                                        5.2Kbp
                                                                                                                                                        401.9Mbp
                                                                                                                                                        229.0
                                                                                                                                                        73.92
                                                                                                                                                        8.44
                                                                                                                                                        13.1%
                                                                                                                                                        egpg5305920.assemble_contigs
                                                                                                                                                        1.3Kbp
                                                                                                                                                        0.9Kbp
                                                                                                                                                        473.3K
                                                                                                                                                        962703.0K
                                                                                                                                                        24.5Kbp
                                                                                                                                                        2070.7Mbp
                                                                                                                                                        1454.0
                                                                                                                                                        86.94
                                                                                                                                                        12.59
                                                                                                                                                        66.7%
                                                                                                                                                        egpg5305936.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        255.6K
                                                                                                                                                        437117.0K
                                                                                                                                                        8.6Kbp
                                                                                                                                                        451.7Mbp
                                                                                                                                                        349.0
                                                                                                                                                        77.77
                                                                                                                                                        8.80
                                                                                                                                                        14.7%
                                                                                                                                                        egpg5305937.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        349.4K
                                                                                                                                                        603841.0K
                                                                                                                                                        4.8Kbp
                                                                                                                                                        652.4Mbp
                                                                                                                                                        342.0
                                                                                                                                                        74.32
                                                                                                                                                        8.98
                                                                                                                                                        21.2%
                                                                                                                                                        egpg5305944.assemble_contigs
                                                                                                                                                        0.8Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        305.4K
                                                                                                                                                        539778.0K
                                                                                                                                                        10.0Kbp
                                                                                                                                                        634.0Mbp
                                                                                                                                                        334.0
                                                                                                                                                        77.69
                                                                                                                                                        10.19
                                                                                                                                                        20.6%
                                                                                                                                                        egpg5305945.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        327.8K
                                                                                                                                                        568616.0K
                                                                                                                                                        6.2Kbp
                                                                                                                                                        622.2Mbp
                                                                                                                                                        299.0
                                                                                                                                                        76.16
                                                                                                                                                        9.62
                                                                                                                                                        20.3%
                                                                                                                                                        egpg5305949.assemble_contigs
                                                                                                                                                        1.3Kbp
                                                                                                                                                        0.8Kbp
                                                                                                                                                        482.7K
                                                                                                                                                        975338.0K
                                                                                                                                                        45.4Kbp
                                                                                                                                                        2036.2Mbp
                                                                                                                                                        1581.0
                                                                                                                                                        86.48
                                                                                                                                                        12.03
                                                                                                                                                        65.5%
                                                                                                                                                        egpg5305952.assemble_contigs
                                                                                                                                                        0.8Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        378.1K
                                                                                                                                                        669546.0K
                                                                                                                                                        4.8Kbp
                                                                                                                                                        792.3Mbp
                                                                                                                                                        380.0
                                                                                                                                                        76.85
                                                                                                                                                        9.69
                                                                                                                                                        25.7%
                                                                                                                                                        egpg5305953.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        345.6K
                                                                                                                                                        593350.0K
                                                                                                                                                        5.9Kbp
                                                                                                                                                        627.3Mbp
                                                                                                                                                        316.0
                                                                                                                                                        74.67
                                                                                                                                                        8.85
                                                                                                                                                        20.4%
                                                                                                                                                        egpg5305959.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        218.9K
                                                                                                                                                        369261.0K
                                                                                                                                                        5.9Kbp
                                                                                                                                                        364.6Mbp
                                                                                                                                                        251.0
                                                                                                                                                        76.77
                                                                                                                                                        8.35
                                                                                                                                                        11.9%
                                                                                                                                                        egpg5305960.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        190.5K
                                                                                                                                                        321243.0K
                                                                                                                                                        6.2Kbp
                                                                                                                                                        317.2Mbp
                                                                                                                                                        232.0
                                                                                                                                                        75.86
                                                                                                                                                        8.33
                                                                                                                                                        10.3%
                                                                                                                                                        egpg5305961.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        296.0K
                                                                                                                                                        505352.0K
                                                                                                                                                        7.3Kbp
                                                                                                                                                        521.3Mbp
                                                                                                                                                        311.0
                                                                                                                                                        75.21
                                                                                                                                                        8.69
                                                                                                                                                        17.0%
                                                                                                                                                        egpg5305967.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        257.4K
                                                                                                                                                        436837.0K
                                                                                                                                                        7.2Kbp
                                                                                                                                                        440.7Mbp
                                                                                                                                                        294.0
                                                                                                                                                        75.46
                                                                                                                                                        8.47
                                                                                                                                                        14.4%
                                                                                                                                                        egpg5305968.assemble_contigs
                                                                                                                                                        0.7Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        218.9K
                                                                                                                                                        368770.0K
                                                                                                                                                        7.6Kbp
                                                                                                                                                        362.6Mbp
                                                                                                                                                        212.0
                                                                                                                                                        73.78
                                                                                                                                                        8.63
                                                                                                                                                        11.8%
                                                                                                                                                        egpg5305969.assemble_contigs
                                                                                                                                                        0.6Kbp
                                                                                                                                                        0.6Kbp
                                                                                                                                                        197.6K
                                                                                                                                                        330653.0K
                                                                                                                                                        6.8Kbp
                                                                                                                                                        317.6Mbp
                                                                                                                                                        226.0
                                                                                                                                                        73.47
                                                                                                                                                        8.17
                                                                                                                                                        10.4%
                                                                                                                                                        egpg5305974.assemble_contigs
                                                                                                                                                        1.5Kbp
                                                                                                                                                        0.9Kbp
                                                                                                                                                        446.3K
                                                                                                                                                        927781.0K
                                                                                                                                                        30.1Kbp
                                                                                                                                                        2292.4Mbp
                                                                                                                                                        1672.0
                                                                                                                                                        87.41
                                                                                                                                                        13.45
                                                                                                                                                        73.6%
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                                                                                                                                                        - Number of Contigs - -

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                                                                                                                                                        BUSCO

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                                                                                                                                                        BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

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                                                                                                                                                              - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                              - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                              - Bioinformatics (2016)
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                                                                                                                                                              About MultiQC

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                                                                                                                                                              This report was generated using MultiQC, version 1.9

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                                                                                                                                                              You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                                                                              MultiQC is published in Bioinformatics:

                                                                                                                                                              -
                                                                                                                                                              - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                              - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                              - Bioinformatics (2016)
                                                                                                                                                              - doi: 10.1093/bioinformatics/btw354
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                                                                                                                                                              - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                                              Report - - generated on 2022-03-30, 11:10 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/EANS

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                                                                                                                                                              General Statistics

                                                                                                                                                              - - - - - - - - - - Showing 64/64 rows and 2/2 columns. - -
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                                                                                                                                                              - -
                                                                                                                                                              Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                                              10_UO_113T_150731_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1884.2Mbp
                                                                                                                                                              12_UO_125T_150731_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              824.2Mbp
                                                                                                                                                              13_UO_134T_150731_L005.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              2074.9Mbp
                                                                                                                                                              14_UO_136T_150731_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              869.8Mbp
                                                                                                                                                              15_UO_140T_150731_L006.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1568.7Mbp
                                                                                                                                                              16_UO_142T_150731_L006.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              1935.3Mbp
                                                                                                                                                              17_UO_144T_150731_L007.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              1974.7Mbp
                                                                                                                                                              18_UO_148T_150731_L007.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1510.0Mbp
                                                                                                                                                              19_UO_153T_150813_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1584.2Mbp
                                                                                                                                                              1_UO_005T_150730_L001.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              1925.3Mbp
                                                                                                                                                              20_UO_157T_150813_L001.assemble_contigs
                                                                                                                                                              0.8Kbp
                                                                                                                                                              504.5Mbp
                                                                                                                                                              21_UO_006C_150813_L002.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1479.7Mbp
                                                                                                                                                              22_UO_045C_150813_L002.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              1943.6Mbp
                                                                                                                                                              23_UO_064C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1657.0Mbp
                                                                                                                                                              24_UO_065C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1617.2Mbp
                                                                                                                                                              25_UO_068C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1690.0Mbp
                                                                                                                                                              26_UO_070C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1646.9Mbp
                                                                                                                                                              27_UO_072C_150813_L001.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              1999.4Mbp
                                                                                                                                                              28_UO_073C_150813_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1621.7Mbp
                                                                                                                                                              29_UO_075C_150813_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1031.5Mbp
                                                                                                                                                              2_UO_044T_150730_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1579.6Mbp
                                                                                                                                                              30_UO_077C_150813_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1830.0Mbp
                                                                                                                                                              31_UO_079C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1507.7Mbp
                                                                                                                                                              32_UO_080C_150813_L003.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              123.2Mbp
                                                                                                                                                              33_UO_082C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1782.2Mbp
                                                                                                                                                              34_UO_088C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1740.8Mbp
                                                                                                                                                              35_UO_090C_150813_L005.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              1912.0Mbp
                                                                                                                                                              36_UO_091C_150813_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1726.7Mbp
                                                                                                                                                              37_UO_092C_150902_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1762.9Mbp
                                                                                                                                                              38_UO_093C_150902_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1779.9Mbp
                                                                                                                                                              39_UO_098C_150902_L002.assemble_contigs
                                                                                                                                                              1.7Kbp
                                                                                                                                                              2181.8Mbp
                                                                                                                                                              3_UO_046T_150730_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1684.3Mbp
                                                                                                                                                              40_UO_099C_150902_L002.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              363.7Mbp
                                                                                                                                                              41_UO_100C_150902_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              969.3Mbp
                                                                                                                                                              42_UO_105C_150902_L003.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              2035.2Mbp
                                                                                                                                                              43_UO_106C_150902_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1878.4Mbp
                                                                                                                                                              44_UO_107C_150902_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1873.6Mbp
                                                                                                                                                              45_UO_109C_150902_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1090.4Mbp
                                                                                                                                                              46_UO_114C_150902_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              770.6Mbp
                                                                                                                                                              47_UO_115C_150902_L006.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              1989.4Mbp
                                                                                                                                                              48_UO_127C_150902_L006.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              650.3Mbp
                                                                                                                                                              49_UO_137C_150902_L007.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1653.3Mbp
                                                                                                                                                              4_UO_048T_150730_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1051.0Mbp
                                                                                                                                                              50_UO_185C_150902_L007.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1817.0Mbp
                                                                                                                                                              5_UO_063T_150731_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1530.7Mbp
                                                                                                                                                              6_UO_069T_150731_L001.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              2055.9Mbp
                                                                                                                                                              7_UO_071T_150731_L002.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              1914.9Mbp
                                                                                                                                                              8_UO_074T_150731_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1864.2Mbp
                                                                                                                                                              9_UO_076T_150731_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              1788.7Mbp
                                                                                                                                                              LP6005442_DNA_F09.assemble_contigs
                                                                                                                                                              0.9Kbp
                                                                                                                                                              1811.0Mbp
                                                                                                                                                              LP6005443_DNA_E06.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1840.8Mbp
                                                                                                                                                              LP6005443_DNA_F06.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              2166.7Mbp
                                                                                                                                                              LP6005677_DNA_G01.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              1814.6Mbp
                                                                                                                                                              egpg5305767.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              199.8Mbp
                                                                                                                                                              egpg5305775.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              124.8Mbp
                                                                                                                                                              egpg5305776.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              186.1Mbp
                                                                                                                                                              egpg5305783.assemble_contigs
                                                                                                                                                              0.8Kbp
                                                                                                                                                              464.6Mbp
                                                                                                                                                              egpg5305791.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              319.5Mbp
                                                                                                                                                              egpg5305792.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              22.6Mbp
                                                                                                                                                              egpg5305793.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              432.2Mbp
                                                                                                                                                              egpg5305798.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              311.8Mbp
                                                                                                                                                              egpg5305799.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              452.5Mbp
                                                                                                                                                              egpg5305814.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              2039.1Mbp
                                                                                                                                                              egpg5305831.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              459.8Mbp
                                                                                                                                                              - - -
                                                                                                                                                              - - - - - - -
                                                                                                                                                              -

                                                                                                                                                              QUAST

                                                                                                                                                              -

                                                                                                                                                              QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                                                                                                                                              - - - - -
                                                                                                                                                              - -

                                                                                                                                                              - Assembly Statistics - -

                                                                                                                                                              - - - - -
                                                                                                                                                              - - - - - - - - - Showing 64/64 rows and 10/10 columns. - -
                                                                                                                                                              -
                                                                                                                                                              - -
                                                                                                                                                              Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                                              10_UO_113T_150731_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              546.5K
                                                                                                                                                              1056668.0K
                                                                                                                                                              13.2Kbp
                                                                                                                                                              1884.2Mbp
                                                                                                                                                              1499.0
                                                                                                                                                              95.00
                                                                                                                                                              13.57
                                                                                                                                                              60.8%
                                                                                                                                                              12_UO_125T_150731_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              217.0K
                                                                                                                                                              447691.0K
                                                                                                                                                              23.5Kbp
                                                                                                                                                              824.2Mbp
                                                                                                                                                              947.0
                                                                                                                                                              111.53
                                                                                                                                                              14.00
                                                                                                                                                              26.5%
                                                                                                                                                              13_UO_134T_150731_L005.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.9Kbp
                                                                                                                                                              478.2K
                                                                                                                                                              965176.0K
                                                                                                                                                              21.8Kbp
                                                                                                                                                              2074.9Mbp
                                                                                                                                                              1534.0
                                                                                                                                                              98.68
                                                                                                                                                              14.20
                                                                                                                                                              66.7%
                                                                                                                                                              14_UO_136T_150731_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              232.3K
                                                                                                                                                              476484.0K
                                                                                                                                                              35.5Kbp
                                                                                                                                                              869.8Mbp
                                                                                                                                                              945.0
                                                                                                                                                              108.97
                                                                                                                                                              13.85
                                                                                                                                                              28.0%
                                                                                                                                                              15_UO_140T_150731_L006.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              511.1K
                                                                                                                                                              970558.0K
                                                                                                                                                              11.2Kbp
                                                                                                                                                              1568.7Mbp
                                                                                                                                                              1244.0
                                                                                                                                                              97.24
                                                                                                                                                              12.52
                                                                                                                                                              50.7%
                                                                                                                                                              16_UO_142T_150731_L006.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              538.8K
                                                                                                                                                              1048888.0K
                                                                                                                                                              13.5Kbp
                                                                                                                                                              1935.3Mbp
                                                                                                                                                              1531.0
                                                                                                                                                              95.57
                                                                                                                                                              13.68
                                                                                                                                                              62.4%
                                                                                                                                                              17_UO_144T_150731_L007.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              491.4K
                                                                                                                                                              979240.0K
                                                                                                                                                              15.4Kbp
                                                                                                                                                              1974.7Mbp
                                                                                                                                                              1463.0
                                                                                                                                                              98.24
                                                                                                                                                              14.19
                                                                                                                                                              63.6%
                                                                                                                                                              18_UO_148T_150731_L007.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              417.8K
                                                                                                                                                              825230.0K
                                                                                                                                                              16.4Kbp
                                                                                                                                                              1510.0Mbp
                                                                                                                                                              1295.0
                                                                                                                                                              101.32
                                                                                                                                                              13.39
                                                                                                                                                              48.7%
                                                                                                                                                              19_UO_153T_150813_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              520.2K
                                                                                                                                                              986962.0K
                                                                                                                                                              12.5Kbp
                                                                                                                                                              1584.2Mbp
                                                                                                                                                              1271.0
                                                                                                                                                              94.22
                                                                                                                                                              13.05
                                                                                                                                                              51.2%
                                                                                                                                                              1_UO_005T_150730_L001.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              497.1K
                                                                                                                                                              984211.0K
                                                                                                                                                              12.8Kbp
                                                                                                                                                              1925.3Mbp
                                                                                                                                                              1691.0
                                                                                                                                                              97.60
                                                                                                                                                              14.00
                                                                                                                                                              62.0%
                                                                                                                                                              20_UO_157T_150813_L001.assemble_contigs
                                                                                                                                                              0.8Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              196.6K
                                                                                                                                                              373848.0K
                                                                                                                                                              15.7Kbp
                                                                                                                                                              504.5Mbp
                                                                                                                                                              1328.0
                                                                                                                                                              114.21
                                                                                                                                                              15.93
                                                                                                                                                              16.3%
                                                                                                                                                              21_UO_006C_150813_L002.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              519.7K
                                                                                                                                                              974007.0K
                                                                                                                                                              15.1Kbp
                                                                                                                                                              1479.7Mbp
                                                                                                                                                              1239.0
                                                                                                                                                              91.82
                                                                                                                                                              13.03
                                                                                                                                                              47.9%
                                                                                                                                                              22_UO_045C_150813_L002.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              478.2K
                                                                                                                                                              957252.0K
                                                                                                                                                              15.8Kbp
                                                                                                                                                              1943.6Mbp
                                                                                                                                                              1493.0
                                                                                                                                                              98.16
                                                                                                                                                              14.30
                                                                                                                                                              62.5%
                                                                                                                                                              23_UO_064C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              547.7K
                                                                                                                                                              1033783.0K
                                                                                                                                                              9.8Kbp
                                                                                                                                                              1657.0Mbp
                                                                                                                                                              1265.0
                                                                                                                                                              93.05
                                                                                                                                                              13.22
                                                                                                                                                              53.6%
                                                                                                                                                              24_UO_065C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              557.4K
                                                                                                                                                              1044179.0K
                                                                                                                                                              11.5Kbp
                                                                                                                                                              1617.2Mbp
                                                                                                                                                              1393.0
                                                                                                                                                              94.07
                                                                                                                                                              12.61
                                                                                                                                                              52.3%
                                                                                                                                                              25_UO_068C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              526.9K
                                                                                                                                                              1006518.0K
                                                                                                                                                              14.6Kbp
                                                                                                                                                              1690.0Mbp
                                                                                                                                                              1368.0
                                                                                                                                                              95.64
                                                                                                                                                              13.42
                                                                                                                                                              54.6%
                                                                                                                                                              26_UO_070C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              496.7K
                                                                                                                                                              958266.0K
                                                                                                                                                              13.1Kbp
                                                                                                                                                              1646.9Mbp
                                                                                                                                                              1329.0
                                                                                                                                                              95.51
                                                                                                                                                              13.60
                                                                                                                                                              53.2%
                                                                                                                                                              27_UO_072C_150813_L001.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              501.3K
                                                                                                                                                              994548.0K
                                                                                                                                                              23.5Kbp
                                                                                                                                                              1999.4Mbp
                                                                                                                                                              1492.0
                                                                                                                                                              98.14
                                                                                                                                                              14.28
                                                                                                                                                              64.4%
                                                                                                                                                              28_UO_073C_150813_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              527.3K
                                                                                                                                                              1000296.0K
                                                                                                                                                              13.3Kbp
                                                                                                                                                              1621.7Mbp
                                                                                                                                                              1339.0
                                                                                                                                                              94.93
                                                                                                                                                              13.23
                                                                                                                                                              52.4%
                                                                                                                                                              29_UO_075C_150813_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              293.6K
                                                                                                                                                              586086.0K
                                                                                                                                                              16.1Kbp
                                                                                                                                                              1031.5Mbp
                                                                                                                                                              1057.0
                                                                                                                                                              105.81
                                                                                                                                                              13.33
                                                                                                                                                              33.3%
                                                                                                                                                              2_UO_044T_150730_L001.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              497.7K
                                                                                                                                                              953704.0K
                                                                                                                                                              11.9Kbp
                                                                                                                                                              1579.6Mbp
                                                                                                                                                              1363.0
                                                                                                                                                              95.17
                                                                                                                                                              13.46
                                                                                                                                                              51.1%
                                                                                                                                                              30_UO_077C_150813_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              520.0K
                                                                                                                                                              1012758.0K
                                                                                                                                                              13.6Kbp
                                                                                                                                                              1830.0Mbp
                                                                                                                                                              1356.0
                                                                                                                                                              94.87
                                                                                                                                                              13.47
                                                                                                                                                              59.0%
                                                                                                                                                              31_UO_079C_150813_L003.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              534.2K
                                                                                                                                                              996186.0K
                                                                                                                                                              12.0Kbp
                                                                                                                                                              1507.7Mbp
                                                                                                                                                              1230.0
                                                                                                                                                              92.39
                                                                                                                                                              12.27
                                                                                                                                                              48.8%
                                                                                                                                                              32_UO_080C_150813_L003.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              30.1K
                                                                                                                                                              60128.0K
                                                                                                                                                              16.7Kbp
                                                                                                                                                              123.2Mbp
                                                                                                                                                              47.0
                                                                                                                                                              86.10
                                                                                                                                                              12.80
                                                                                                                                                              4.0%
                                                                                                                                                              33_UO_082C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              500.3K
                                                                                                                                                              979293.0K
                                                                                                                                                              11.6Kbp
                                                                                                                                                              1782.2Mbp
                                                                                                                                                              1365.0
                                                                                                                                                              96.54
                                                                                                                                                              13.70
                                                                                                                                                              57.5%
                                                                                                                                                              34_UO_088C_150813_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              523.6K
                                                                                                                                                              1008279.0K
                                                                                                                                                              11.4Kbp
                                                                                                                                                              1740.8Mbp
                                                                                                                                                              1427.0
                                                                                                                                                              95.73
                                                                                                                                                              13.57
                                                                                                                                                              56.2%
                                                                                                                                                              35_UO_090C_150813_L005.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              510.7K
                                                                                                                                                              1002879.0K
                                                                                                                                                              13.6Kbp
                                                                                                                                                              1912.0Mbp
                                                                                                                                                              1594.0
                                                                                                                                                              97.62
                                                                                                                                                              13.92
                                                                                                                                                              61.6%
                                                                                                                                                              36_UO_091C_150813_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              530.7K
                                                                                                                                                              1015400.0K
                                                                                                                                                              12.3Kbp
                                                                                                                                                              1726.7Mbp
                                                                                                                                                              1380.0
                                                                                                                                                              95.95
                                                                                                                                                              13.41
                                                                                                                                                              55.8%
                                                                                                                                                              37_UO_092C_150902_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              536.3K
                                                                                                                                                              1027662.0K
                                                                                                                                                              15.0Kbp
                                                                                                                                                              1762.9Mbp
                                                                                                                                                              1459.0
                                                                                                                                                              96.73
                                                                                                                                                              13.52
                                                                                                                                                              56.9%
                                                                                                                                                              38_UO_093C_150902_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              535.9K
                                                                                                                                                              1028739.0K
                                                                                                                                                              13.9Kbp
                                                                                                                                                              1779.9Mbp
                                                                                                                                                              1601.0
                                                                                                                                                              97.39
                                                                                                                                                              13.83
                                                                                                                                                              57.4%
                                                                                                                                                              39_UO_098C_150902_L002.assemble_contigs
                                                                                                                                                              1.7Kbp
                                                                                                                                                              1.0Kbp
                                                                                                                                                              376.8K
                                                                                                                                                              805016.0K
                                                                                                                                                              24.9Kbp
                                                                                                                                                              2181.8Mbp
                                                                                                                                                              1622.0
                                                                                                                                                              101.30
                                                                                                                                                              14.27
                                                                                                                                                              70.1%
                                                                                                                                                              3_UO_046T_150730_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              524.4K
                                                                                                                                                              1002311.0K
                                                                                                                                                              11.6Kbp
                                                                                                                                                              1684.3Mbp
                                                                                                                                                              1348.0
                                                                                                                                                              97.28
                                                                                                                                                              13.07
                                                                                                                                                              54.4%
                                                                                                                                                              40_UO_099C_150902_L002.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              200.7K
                                                                                                                                                              344164.0K
                                                                                                                                                              5.8Kbp
                                                                                                                                                              363.7Mbp
                                                                                                                                                              429.0
                                                                                                                                                              89.43
                                                                                                                                                              11.23
                                                                                                                                                              11.9%
                                                                                                                                                              41_UO_100C_150902_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              266.8K
                                                                                                                                                              540620.0K
                                                                                                                                                              19.0Kbp
                                                                                                                                                              969.3Mbp
                                                                                                                                                              940.0
                                                                                                                                                              107.91
                                                                                                                                                              14.30
                                                                                                                                                              31.3%
                                                                                                                                                              42_UO_105C_150902_L003.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              508.3K
                                                                                                                                                              1007910.0K
                                                                                                                                                              21.7Kbp
                                                                                                                                                              2035.2Mbp
                                                                                                                                                              1542.0
                                                                                                                                                              98.82
                                                                                                                                                              14.17
                                                                                                                                                              65.5%
                                                                                                                                                              43_UO_106C_150902_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              533.7K
                                                                                                                                                              1035125.0K
                                                                                                                                                              13.2Kbp
                                                                                                                                                              1878.4Mbp
                                                                                                                                                              1433.0
                                                                                                                                                              97.64
                                                                                                                                                              13.87
                                                                                                                                                              60.6%
                                                                                                                                                              44_UO_107C_150902_L004.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              535.9K
                                                                                                                                                              1037954.0K
                                                                                                                                                              13.2Kbp
                                                                                                                                                              1873.6Mbp
                                                                                                                                                              1552.0
                                                                                                                                                              97.02
                                                                                                                                                              13.66
                                                                                                                                                              60.4%
                                                                                                                                                              45_UO_109C_150902_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              296.2K
                                                                                                                                                              599519.0K
                                                                                                                                                              21.9Kbp
                                                                                                                                                              1090.4Mbp
                                                                                                                                                              1117.0
                                                                                                                                                              106.88
                                                                                                                                                              13.72
                                                                                                                                                              35.1%
                                                                                                                                                              46_UO_114C_150902_L005.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              197.4K
                                                                                                                                                              411196.0K
                                                                                                                                                              27.9Kbp
                                                                                                                                                              770.6Mbp
                                                                                                                                                              938.0
                                                                                                                                                              111.36
                                                                                                                                                              14.26
                                                                                                                                                              24.8%
                                                                                                                                                              47_UO_115C_150902_L006.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              532.8K
                                                                                                                                                              1041725.0K
                                                                                                                                                              14.4Kbp
                                                                                                                                                              1989.4Mbp
                                                                                                                                                              1536.0
                                                                                                                                                              96.12
                                                                                                                                                              13.63
                                                                                                                                                              64.1%
                                                                                                                                                              48_UO_127C_150902_L006.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              187.6K
                                                                                                                                                              384482.0K
                                                                                                                                                              30.5Kbp
                                                                                                                                                              650.3Mbp
                                                                                                                                                              1157.0
                                                                                                                                                              114.74
                                                                                                                                                              14.78
                                                                                                                                                              20.9%
                                                                                                                                                              49_UO_137C_150902_L007.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              574.9K
                                                                                                                                                              1074422.0K
                                                                                                                                                              12.2Kbp
                                                                                                                                                              1653.3Mbp
                                                                                                                                                              1342.0
                                                                                                                                                              93.12
                                                                                                                                                              13.02
                                                                                                                                                              53.5%
                                                                                                                                                              4_UO_048T_150730_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              269.2K
                                                                                                                                                              555536.0K
                                                                                                                                                              27.5Kbp
                                                                                                                                                              1051.0Mbp
                                                                                                                                                              1002.0
                                                                                                                                                              107.75
                                                                                                                                                              14.45
                                                                                                                                                              33.9%
                                                                                                                                                              50_UO_185C_150902_L007.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              515.1K
                                                                                                                                                              1006278.0K
                                                                                                                                                              16.1Kbp
                                                                                                                                                              1817.0Mbp
                                                                                                                                                              1338.0
                                                                                                                                                              96.80
                                                                                                                                                              13.73
                                                                                                                                                              58.6%
                                                                                                                                                              5_UO_063T_150731_L001.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              434.6K
                                                                                                                                                              854502.0K
                                                                                                                                                              15.5Kbp
                                                                                                                                                              1530.7Mbp
                                                                                                                                                              1231.0
                                                                                                                                                              101.17
                                                                                                                                                              13.24
                                                                                                                                                              49.4%
                                                                                                                                                              6_UO_069T_150731_L001.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.9Kbp
                                                                                                                                                              468.4K
                                                                                                                                                              949454.0K
                                                                                                                                                              18.4Kbp
                                                                                                                                                              2055.9Mbp
                                                                                                                                                              1501.0
                                                                                                                                                              98.67
                                                                                                                                                              14.34
                                                                                                                                                              66.1%
                                                                                                                                                              7_UO_071T_150731_L002.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              516.7K
                                                                                                                                                              1012133.0K
                                                                                                                                                              13.6Kbp
                                                                                                                                                              1914.9Mbp
                                                                                                                                                              1413.0
                                                                                                                                                              97.86
                                                                                                                                                              13.75
                                                                                                                                                              61.7%
                                                                                                                                                              8_UO_074T_150731_L002.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              519.1K
                                                                                                                                                              1015134.0K
                                                                                                                                                              13.8Kbp
                                                                                                                                                              1864.2Mbp
                                                                                                                                                              1471.0
                                                                                                                                                              95.18
                                                                                                                                                              13.45
                                                                                                                                                              60.1%
                                                                                                                                                              9_UO_076T_150731_L003.assemble_contigs
                                                                                                                                                              1.1Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              529.6K
                                                                                                                                                              1023588.0K
                                                                                                                                                              11.8Kbp
                                                                                                                                                              1788.7Mbp
                                                                                                                                                              1386.0
                                                                                                                                                              94.74
                                                                                                                                                              13.35
                                                                                                                                                              57.8%
                                                                                                                                                              LP6005442_DNA_F09.assemble_contigs
                                                                                                                                                              0.9Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              654.6K
                                                                                                                                                              1226660.0K
                                                                                                                                                              10.2Kbp
                                                                                                                                                              1811.0Mbp
                                                                                                                                                              907.0
                                                                                                                                                              77.25
                                                                                                                                                              11.93
                                                                                                                                                              57.9%
                                                                                                                                                              LP6005443_DNA_E06.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              617.3K
                                                                                                                                                              1172269.0K
                                                                                                                                                              15.2Kbp
                                                                                                                                                              1840.8Mbp
                                                                                                                                                              846.0
                                                                                                                                                              76.18
                                                                                                                                                              11.95
                                                                                                                                                              58.8%
                                                                                                                                                              LP6005443_DNA_F06.assemble_contigs
                                                                                                                                                              1.3Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              512.7K
                                                                                                                                                              1044461.0K
                                                                                                                                                              18.4Kbp
                                                                                                                                                              2166.7Mbp
                                                                                                                                                              1208.0
                                                                                                                                                              82.48
                                                                                                                                                              13.39
                                                                                                                                                              69.2%
                                                                                                                                                              LP6005677_DNA_G01.assemble_contigs
                                                                                                                                                              1.0Kbp
                                                                                                                                                              0.7Kbp
                                                                                                                                                              639.4K
                                                                                                                                                              1199146.0K
                                                                                                                                                              10.1Kbp
                                                                                                                                                              1814.6Mbp
                                                                                                                                                              919.0
                                                                                                                                                              79.29
                                                                                                                                                              12.01
                                                                                                                                                              58.0%
                                                                                                                                                              egpg5305767.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              126.7K
                                                                                                                                                              211776.0K
                                                                                                                                                              11.2Kbp
                                                                                                                                                              199.8Mbp
                                                                                                                                                              250.0
                                                                                                                                                              87.36
                                                                                                                                                              9.42
                                                                                                                                                              6.5%
                                                                                                                                                              egpg5305775.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              76.0K
                                                                                                                                                              128143.0K
                                                                                                                                                              3.3Kbp
                                                                                                                                                              124.8Mbp
                                                                                                                                                              97.0
                                                                                                                                                              87.26
                                                                                                                                                              9.76
                                                                                                                                                              4.1%
                                                                                                                                                              egpg5305776.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              115.2K
                                                                                                                                                              193341.0K
                                                                                                                                                              3.9Kbp
                                                                                                                                                              186.1Mbp
                                                                                                                                                              152.0
                                                                                                                                                              84.62
                                                                                                                                                              8.99
                                                                                                                                                              6.1%
                                                                                                                                                              egpg5305783.assemble_contigs
                                                                                                                                                              0.8Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              221.6K
                                                                                                                                                              394385.0K
                                                                                                                                                              7.4Kbp
                                                                                                                                                              464.6Mbp
                                                                                                                                                              276.0
                                                                                                                                                              88.05
                                                                                                                                                              9.91
                                                                                                                                                              15.1%
                                                                                                                                                              egpg5305791.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              164.4K
                                                                                                                                                              287861.0K
                                                                                                                                                              5.3Kbp
                                                                                                                                                              319.5Mbp
                                                                                                                                                              195.0
                                                                                                                                                              87.95
                                                                                                                                                              10.09
                                                                                                                                                              10.4%
                                                                                                                                                              egpg5305792.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              0.5Kbp
                                                                                                                                                              15.8K
                                                                                                                                                              25901.0K
                                                                                                                                                              10.8Kbp
                                                                                                                                                              22.6Mbp
                                                                                                                                                              50.0
                                                                                                                                                              105.37
                                                                                                                                                              18.38
                                                                                                                                                              0.7%
                                                                                                                                                              egpg5305793.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              227.5K
                                                                                                                                                              395670.0K
                                                                                                                                                              5.1Kbp
                                                                                                                                                              432.2Mbp
                                                                                                                                                              286.0
                                                                                                                                                              84.68
                                                                                                                                                              9.37
                                                                                                                                                              14.1%
                                                                                                                                                              egpg5305798.assemble_contigs
                                                                                                                                                              0.6Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              193.5K
                                                                                                                                                              324193.0K
                                                                                                                                                              8.1Kbp
                                                                                                                                                              311.8Mbp
                                                                                                                                                              273.0
                                                                                                                                                              80.45
                                                                                                                                                              8.60
                                                                                                                                                              10.2%
                                                                                                                                                              egpg5305799.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              219.9K
                                                                                                                                                              389634.0K
                                                                                                                                                              5.6Kbp
                                                                                                                                                              452.5Mbp
                                                                                                                                                              263.0
                                                                                                                                                              87.04
                                                                                                                                                              9.97
                                                                                                                                                              14.7%
                                                                                                                                                              egpg5305814.assemble_contigs
                                                                                                                                                              1.2Kbp
                                                                                                                                                              0.8Kbp
                                                                                                                                                              509.6K
                                                                                                                                                              1020495.0K
                                                                                                                                                              43.5Kbp
                                                                                                                                                              2039.1Mbp
                                                                                                                                                              1556.0
                                                                                                                                                              91.98
                                                                                                                                                              12.77
                                                                                                                                                              65.6%
                                                                                                                                                              egpg5305831.assemble_contigs
                                                                                                                                                              0.7Kbp
                                                                                                                                                              0.6Kbp
                                                                                                                                                              246.9K
                                                                                                                                                              427225.0K
                                                                                                                                                              10.9Kbp
                                                                                                                                                              459.8Mbp
                                                                                                                                                              295.0
                                                                                                                                                              84.19
                                                                                                                                                              9.34
                                                                                                                                                              15.0%
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                                                                                                                                                              - Number of Contigs - -

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                                                                                                                                                                    About MultiQC

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                                                                                                                                                                    This report was generated using MultiQC, version 1.9

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                                                                                                                                                                    MultiQC is published in Bioinformatics:

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                                                                                                                                                                    - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                                    - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                                    - Bioinformatics (2016)
                                                                                                                                                                    - doi: 10.1093/bioinformatics/btw354
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                                                                                                                                                                    - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                                                    Report - - generated on 2022-03-30, 11:11 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/FWNC

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                                                                                                                                                                    General Statistics

                                                                                                                                                                    - - - - - - - - - - Showing 35/35 rows and 2/2 columns. - -
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                                                                                                                                                                    Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                                                    HG03225.assemble_contigs
                                                                                                                                                                    8.3Kbp
                                                                                                                                                                    2722.4Mbp
                                                                                                                                                                    HG03380.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    2705.7Mbp
                                                                                                                                                                    HG03385.assemble_contigs
                                                                                                                                                                    9.7Kbp
                                                                                                                                                                    2749.9Mbp
                                                                                                                                                                    HG03388.assemble_contigs
                                                                                                                                                                    8.3Kbp
                                                                                                                                                                    2720.8Mbp
                                                                                                                                                                    HG03449.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    2705.0Mbp
                                                                                                                                                                    IAJ0K.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    2673.4Mbp
                                                                                                                                                                    IAM0N.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    2674.2Mbp
                                                                                                                                                                    IAP0Q.assemble_contigs
                                                                                                                                                                    6.5Kbp
                                                                                                                                                                    2694.4Mbp
                                                                                                                                                                    IBJ0M.assemble_contigs
                                                                                                                                                                    6.3Kbp
                                                                                                                                                                    2673.2Mbp
                                                                                                                                                                    IBQ0T.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    2675.8Mbp
                                                                                                                                                                    LP6005441_DNA_F07.assemble_contigs
                                                                                                                                                                    1.0Kbp
                                                                                                                                                                    1948.4Mbp
                                                                                                                                                                    LZP0B.assemble_contigs
                                                                                                                                                                    6.8Kbp
                                                                                                                                                                    2691.8Mbp
                                                                                                                                                                    NA18498.assemble_contigs
                                                                                                                                                                    7.8Kbp
                                                                                                                                                                    2725.2Mbp
                                                                                                                                                                    NA18499.assemble_contigs
                                                                                                                                                                    10.2Kbp
                                                                                                                                                                    2735.3Mbp
                                                                                                                                                                    NA18501.assemble_contigs
                                                                                                                                                                    7.5Kbp
                                                                                                                                                                    2726.0Mbp
                                                                                                                                                                    NA18504.assemble_contigs
                                                                                                                                                                    8.0Kbp
                                                                                                                                                                    2722.1Mbp
                                                                                                                                                                    NA18505.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    2701.5Mbp
                                                                                                                                                                    NA19099.assemble_contigs
                                                                                                                                                                    8.5Kbp
                                                                                                                                                                    2703.3Mbp
                                                                                                                                                                    NA19107.assemble_contigs
                                                                                                                                                                    9.3Kbp
                                                                                                                                                                    2750.0Mbp
                                                                                                                                                                    NA19118.assemble_contigs
                                                                                                                                                                    8.4Kbp
                                                                                                                                                                    2703.0Mbp
                                                                                                                                                                    NA19129.assemble_contigs
                                                                                                                                                                    10.8Kbp
                                                                                                                                                                    2734.4Mbp
                                                                                                                                                                    NA19131.assemble_contigs
                                                                                                                                                                    12.0Kbp
                                                                                                                                                                    2732.8Mbp
                                                                                                                                                                    PAV0Q.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    2693.0Mbp
                                                                                                                                                                    PAZ0V.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    2677.5Mbp
                                                                                                                                                                    PBA0X.assemble_contigs
                                                                                                                                                                    6.8Kbp
                                                                                                                                                                    2692.6Mbp
                                                                                                                                                                    PBC0A.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    2677.5Mbp
                                                                                                                                                                    SAMEA2580885.assemble_contigs
                                                                                                                                                                    4.9Kbp
                                                                                                                                                                    2720.3Mbp
                                                                                                                                                                    SAMEA2580886.assemble_contigs
                                                                                                                                                                    5.8Kbp
                                                                                                                                                                    2719.7Mbp
                                                                                                                                                                    SAMEA2580889.assemble_contigs
                                                                                                                                                                    5.8Kbp
                                                                                                                                                                    2714.4Mbp
                                                                                                                                                                    SAMEA2580891.assemble_contigs
                                                                                                                                                                    5.9Kbp
                                                                                                                                                                    2699.9Mbp
                                                                                                                                                                    SAMEA2580897.assemble_contigs
                                                                                                                                                                    7.9Kbp
                                                                                                                                                                    2726.5Mbp
                                                                                                                                                                    SAMEA3506075.assemble_contigs
                                                                                                                                                                    10.1Kbp
                                                                                                                                                                    2739.4Mbp
                                                                                                                                                                    SAMEA3506076.assemble_contigs
                                                                                                                                                                    10.8Kbp
                                                                                                                                                                    2722.1Mbp
                                                                                                                                                                    SAMEA3506077.assemble_contigs
                                                                                                                                                                    9.2Kbp
                                                                                                                                                                    2740.3Mbp
                                                                                                                                                                    SAMEA3506078.assemble_contigs
                                                                                                                                                                    7.6Kbp
                                                                                                                                                                    2741.2Mbp
                                                                                                                                                                    - - -
                                                                                                                                                                    - - - - - - -
                                                                                                                                                                    -

                                                                                                                                                                    QUAST

                                                                                                                                                                    -

                                                                                                                                                                    QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                                                                                                                                                    - - - - -
                                                                                                                                                                    - -

                                                                                                                                                                    - Assembly Statistics - -

                                                                                                                                                                    - - - - -
                                                                                                                                                                    - - - - - - - - - Showing 35/35 rows and 10/10 columns. - -
                                                                                                                                                                    -
                                                                                                                                                                    - -
                                                                                                                                                                    Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                                                    HG03225.assemble_contigs
                                                                                                                                                                    8.3Kbp
                                                                                                                                                                    4.3Kbp
                                                                                                                                                                    94.3K
                                                                                                                                                                    207705.0K
                                                                                                                                                                    120.4Kbp
                                                                                                                                                                    2722.4Mbp
                                                                                                                                                                    1692.0
                                                                                                                                                                    109.29
                                                                                                                                                                    21.41
                                                                                                                                                                    88.4%
                                                                                                                                                                    HG03380.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    4.2Kbp
                                                                                                                                                                    96.4K
                                                                                                                                                                    211765.0K
                                                                                                                                                                    137.0Kbp
                                                                                                                                                                    2705.7Mbp
                                                                                                                                                                    1587.0
                                                                                                                                                                    109.02
                                                                                                                                                                    21.21
                                                                                                                                                                    87.8%
                                                                                                                                                                    HG03385.assemble_contigs
                                                                                                                                                                    9.7Kbp
                                                                                                                                                                    5.0Kbp
                                                                                                                                                                    82.1K
                                                                                                                                                                    180547.0K
                                                                                                                                                                    175.1Kbp
                                                                                                                                                                    2749.9Mbp
                                                                                                                                                                    1838.0
                                                                                                                                                                    111.24
                                                                                                                                                                    24.88
                                                                                                                                                                    89.1%
                                                                                                                                                                    HG03388.assemble_contigs
                                                                                                                                                                    8.3Kbp
                                                                                                                                                                    4.3Kbp
                                                                                                                                                                    94.1K
                                                                                                                                                                    207498.0K
                                                                                                                                                                    196.0Kbp
                                                                                                                                                                    2720.8Mbp
                                                                                                                                                                    1697.0
                                                                                                                                                                    109.32
                                                                                                                                                                    21.38
                                                                                                                                                                    88.3%
                                                                                                                                                                    HG03449.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    4.2Kbp
                                                                                                                                                                    96.2K
                                                                                                                                                                    211409.0K
                                                                                                                                                                    129.9Kbp
                                                                                                                                                                    2705.0Mbp
                                                                                                                                                                    1573.0
                                                                                                                                                                    109.28
                                                                                                                                                                    21.15
                                                                                                                                                                    87.8%
                                                                                                                                                                    IAJ0K.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    3.3Kbp
                                                                                                                                                                    121.8K
                                                                                                                                                                    266515.0K
                                                                                                                                                                    69.7Kbp
                                                                                                                                                                    2673.4Mbp
                                                                                                                                                                    625.0
                                                                                                                                                                    103.44
                                                                                                                                                                    20.09
                                                                                                                                                                    86.7%
                                                                                                                                                                    IAM0N.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    3.3Kbp
                                                                                                                                                                    121.9K
                                                                                                                                                                    266615.0K
                                                                                                                                                                    82.8Kbp
                                                                                                                                                                    2674.2Mbp
                                                                                                                                                                    618.0
                                                                                                                                                                    103.26
                                                                                                                                                                    20.09
                                                                                                                                                                    86.7%
                                                                                                                                                                    IAP0Q.assemble_contigs
                                                                                                                                                                    6.5Kbp
                                                                                                                                                                    3.4Kbp
                                                                                                                                                                    119.9K
                                                                                                                                                                    263034.0K
                                                                                                                                                                    81.8Kbp
                                                                                                                                                                    2694.4Mbp
                                                                                                                                                                    684.0
                                                                                                                                                                    103.48
                                                                                                                                                                    20.44
                                                                                                                                                                    87.4%
                                                                                                                                                                    IBJ0M.assemble_contigs
                                                                                                                                                                    6.3Kbp
                                                                                                                                                                    3.3Kbp
                                                                                                                                                                    123.3K
                                                                                                                                                                    269460.0K
                                                                                                                                                                    73.1Kbp
                                                                                                                                                                    2673.2Mbp
                                                                                                                                                                    626.0
                                                                                                                                                                    103.39
                                                                                                                                                                    20.08
                                                                                                                                                                    86.7%
                                                                                                                                                                    IBQ0T.assemble_contigs
                                                                                                                                                                    6.4Kbp
                                                                                                                                                                    3.3Kbp
                                                                                                                                                                    121.5K
                                                                                                                                                                    266101.0K
                                                                                                                                                                    73.7Kbp
                                                                                                                                                                    2675.8Mbp
                                                                                                                                                                    586.0
                                                                                                                                                                    103.15
                                                                                                                                                                    20.18
                                                                                                                                                                    86.8%
                                                                                                                                                                    LP6005441_DNA_F07.assemble_contigs
                                                                                                                                                                    1.0Kbp
                                                                                                                                                                    0.7Kbp
                                                                                                                                                                    665.2K
                                                                                                                                                                    1255240.0K
                                                                                                                                                                    13.4Kbp
                                                                                                                                                                    1948.4Mbp
                                                                                                                                                                    1017.0
                                                                                                                                                                    78.10
                                                                                                                                                                    12.64
                                                                                                                                                                    62.2%
                                                                                                                                                                    LZP0B.assemble_contigs
                                                                                                                                                                    6.8Kbp
                                                                                                                                                                    3.5Kbp
                                                                                                                                                                    114.7K
                                                                                                                                                                    251744.0K
                                                                                                                                                                    77.6Kbp
                                                                                                                                                                    2691.8Mbp
                                                                                                                                                                    607.0
                                                                                                                                                                    103.48
                                                                                                                                                                    20.42
                                                                                                                                                                    87.4%
                                                                                                                                                                    NA18498.assemble_contigs
                                                                                                                                                                    7.8Kbp
                                                                                                                                                                    4.1Kbp
                                                                                                                                                                    100.6K
                                                                                                                                                                    220686.0K
                                                                                                                                                                    114.7Kbp
                                                                                                                                                                    2725.2Mbp
                                                                                                                                                                    1642.0
                                                                                                                                                                    108.34
                                                                                                                                                                    21.29
                                                                                                                                                                    88.4%
                                                                                                                                                                    NA18499.assemble_contigs
                                                                                                                                                                    10.2Kbp
                                                                                                                                                                    5.3Kbp
                                                                                                                                                                    77.9K
                                                                                                                                                                    170989.0K
                                                                                                                                                                    167.8Kbp
                                                                                                                                                                    2735.3Mbp
                                                                                                                                                                    1895.0
                                                                                                                                                                    111.11
                                                                                                                                                                    24.87
                                                                                                                                                                    88.6%
                                                                                                                                                                    NA18501.assemble_contigs
                                                                                                                                                                    7.5Kbp
                                                                                                                                                                    3.9Kbp
                                                                                                                                                                    105.1K
                                                                                                                                                                    231381.0K
                                                                                                                                                                    101.2Kbp
                                                                                                                                                                    2726.0Mbp
                                                                                                                                                                    1719.0
                                                                                                                                                                    108.86
                                                                                                                                                                    21.32
                                                                                                                                                                    88.3%
                                                                                                                                                                    NA18504.assemble_contigs
                                                                                                                                                                    8.0Kbp
                                                                                                                                                                    4.1Kbp
                                                                                                                                                                    98.2K
                                                                                                                                                                    216370.0K
                                                                                                                                                                    118.3Kbp
                                                                                                                                                                    2722.1Mbp
                                                                                                                                                                    1463.0
                                                                                                                                                                    107.57
                                                                                                                                                                    21.28
                                                                                                                                                                    88.3%
                                                                                                                                                                    NA18505.assemble_contigs
                                                                                                                                                                    8.1Kbp
                                                                                                                                                                    4.2Kbp
                                                                                                                                                                    97.1K
                                                                                                                                                                    213471.0K
                                                                                                                                                                    93.3Kbp
                                                                                                                                                                    2701.5Mbp
                                                                                                                                                                    1510.0
                                                                                                                                                                    108.11
                                                                                                                                                                    20.98
                                                                                                                                                                    87.7%
                                                                                                                                                                    NA19099.assemble_contigs
                                                                                                                                                                    8.5Kbp
                                                                                                                                                                    4.4Kbp
                                                                                                                                                                    92.2K
                                                                                                                                                                    202381.0K
                                                                                                                                                                    101.8Kbp
                                                                                                                                                                    2703.3Mbp
                                                                                                                                                                    1579.0
                                                                                                                                                                    107.98
                                                                                                                                                                    20.99
                                                                                                                                                                    87.8%
                                                                                                                                                                    NA19107.assemble_contigs
                                                                                                                                                                    9.3Kbp
                                                                                                                                                                    4.8Kbp
                                                                                                                                                                    85.6K
                                                                                                                                                                    188673.0K
                                                                                                                                                                    111.4Kbp
                                                                                                                                                                    2750.0Mbp
                                                                                                                                                                    1799.0
                                                                                                                                                                    110.58
                                                                                                                                                                    24.62
                                                                                                                                                                    89.0%
                                                                                                                                                                    NA19118.assemble_contigs
                                                                                                                                                                    8.4Kbp
                                                                                                                                                                    4.3Kbp
                                                                                                                                                                    93.3K
                                                                                                                                                                    204862.0K
                                                                                                                                                                    127.5Kbp
                                                                                                                                                                    2703.0Mbp
                                                                                                                                                                    1549.0
                                                                                                                                                                    107.68
                                                                                                                                                                    20.82
                                                                                                                                                                    87.8%
                                                                                                                                                                    NA19129.assemble_contigs
                                                                                                                                                                    10.8Kbp
                                                                                                                                                                    5.6Kbp
                                                                                                                                                                    73.9K
                                                                                                                                                                    161555.0K
                                                                                                                                                                    123.6Kbp
                                                                                                                                                                    2734.4Mbp
                                                                                                                                                                    1892.0
                                                                                                                                                                    111.13
                                                                                                                                                                    24.89
                                                                                                                                                                    88.7%
                                                                                                                                                                    NA19131.assemble_contigs
                                                                                                                                                                    12.0Kbp
                                                                                                                                                                    6.2Kbp
                                                                                                                                                                    66.2K
                                                                                                                                                                    145258.0K
                                                                                                                                                                    133.7Kbp
                                                                                                                                                                    2732.8Mbp
                                                                                                                                                                    1801.0
                                                                                                                                                                    111.39
                                                                                                                                                                    25.10
                                                                                                                                                                    88.7%
                                                                                                                                                                    PAV0Q.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    3.5Kbp
                                                                                                                                                                    116.2K
                                                                                                                                                                    254496.0K
                                                                                                                                                                    86.9Kbp
                                                                                                                                                                    2693.0Mbp
                                                                                                                                                                    648.0
                                                                                                                                                                    103.54
                                                                                                                                                                    20.49
                                                                                                                                                                    87.4%
                                                                                                                                                                    PAZ0V.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    3.5Kbp
                                                                                                                                                                    117.5K
                                                                                                                                                                    256264.0K
                                                                                                                                                                    102.2Kbp
                                                                                                                                                                    2677.5Mbp
                                                                                                                                                                    592.0
                                                                                                                                                                    103.41
                                                                                                                                                                    20.20
                                                                                                                                                                    86.9%
                                                                                                                                                                    PBA0X.assemble_contigs
                                                                                                                                                                    6.8Kbp
                                                                                                                                                                    3.5Kbp
                                                                                                                                                                    114.6K
                                                                                                                                                                    251112.0K
                                                                                                                                                                    82.7Kbp
                                                                                                                                                                    2692.6Mbp
                                                                                                                                                                    635.0
                                                                                                                                                                    103.68
                                                                                                                                                                    20.49
                                                                                                                                                                    87.4%
                                                                                                                                                                    PBC0A.assemble_contigs
                                                                                                                                                                    6.7Kbp
                                                                                                                                                                    3.5Kbp
                                                                                                                                                                    116.9K
                                                                                                                                                                    255057.0K
                                                                                                                                                                    80.9Kbp
                                                                                                                                                                    2677.5Mbp
                                                                                                                                                                    572.0
                                                                                                                                                                    103.63
                                                                                                                                                                    20.27
                                                                                                                                                                    86.9%
                                                                                                                                                                    SAMEA2580885.assemble_contigs
                                                                                                                                                                    4.9Kbp
                                                                                                                                                                    2.5Kbp
                                                                                                                                                                    161.9K
                                                                                                                                                                    355197.0K
                                                                                                                                                                    63.0Kbp
                                                                                                                                                                    2720.3Mbp
                                                                                                                                                                    1826.0
                                                                                                                                                                    108.65
                                                                                                                                                                    20.14
                                                                                                                                                                    87.7%
                                                                                                                                                                    SAMEA2580886.assemble_contigs
                                                                                                                                                                    5.8Kbp
                                                                                                                                                                    3.0Kbp
                                                                                                                                                                    135.7K
                                                                                                                                                                    296941.0K
                                                                                                                                                                    83.8Kbp
                                                                                                                                                                    2719.7Mbp
                                                                                                                                                                    1736.0
                                                                                                                                                                    108.34
                                                                                                                                                                    20.19
                                                                                                                                                                    88.0%
                                                                                                                                                                    SAMEA2580889.assemble_contigs
                                                                                                                                                                    5.8Kbp
                                                                                                                                                                    3.0Kbp
                                                                                                                                                                    135.4K
                                                                                                                                                                    295658.0K
                                                                                                                                                                    87.6Kbp
                                                                                                                                                                    2714.4Mbp
                                                                                                                                                                    1714.0
                                                                                                                                                                    107.94
                                                                                                                                                                    19.88
                                                                                                                                                                    87.9%
                                                                                                                                                                    SAMEA2580891.assemble_contigs
                                                                                                                                                                    5.9Kbp
                                                                                                                                                                    3.1Kbp
                                                                                                                                                                    133.3K
                                                                                                                                                                    290898.0K
                                                                                                                                                                    74.3Kbp
                                                                                                                                                                    2699.9Mbp
                                                                                                                                                                    1598.0
                                                                                                                                                                    108.18
                                                                                                                                                                    19.95
                                                                                                                                                                    87.4%
                                                                                                                                                                    SAMEA2580897.assemble_contigs
                                                                                                                                                                    7.9Kbp
                                                                                                                                                                    4.0Kbp
                                                                                                                                                                    98.5K
                                                                                                                                                                    218360.0K
                                                                                                                                                                    109.4Kbp
                                                                                                                                                                    2726.5Mbp
                                                                                                                                                                    1412.0
                                                                                                                                                                    107.25
                                                                                                                                                                    24.01
                                                                                                                                                                    88.1%
                                                                                                                                                                    SAMEA3506075.assemble_contigs
                                                                                                                                                                    10.1Kbp
                                                                                                                                                                    5.2Kbp
                                                                                                                                                                    78.2K
                                                                                                                                                                    172292.0K
                                                                                                                                                                    122.5Kbp
                                                                                                                                                                    2739.4Mbp
                                                                                                                                                                    1470.0
                                                                                                                                                                    108.36
                                                                                                                                                                    24.30
                                                                                                                                                                    88.8%
                                                                                                                                                                    SAMEA3506076.assemble_contigs
                                                                                                                                                                    10.8Kbp
                                                                                                                                                                    5.5Kbp
                                                                                                                                                                    72.7K
                                                                                                                                                                    160547.0K
                                                                                                                                                                    130.5Kbp
                                                                                                                                                                    2722.1Mbp
                                                                                                                                                                    1406.0
                                                                                                                                                                    108.36
                                                                                                                                                                    24.36
                                                                                                                                                                    88.3%
                                                                                                                                                                    SAMEA3506077.assemble_contigs
                                                                                                                                                                    9.2Kbp
                                                                                                                                                                    4.7Kbp
                                                                                                                                                                    86.3K
                                                                                                                                                                    190186.0K
                                                                                                                                                                    108.3Kbp
                                                                                                                                                                    2740.3Mbp
                                                                                                                                                                    1478.0
                                                                                                                                                                    108.28
                                                                                                                                                                    24.19
                                                                                                                                                                    88.8%
                                                                                                                                                                    SAMEA3506078.assemble_contigs
                                                                                                                                                                    7.6Kbp
                                                                                                                                                                    3.9Kbp
                                                                                                                                                                    102.9K
                                                                                                                                                                    229398.0K
                                                                                                                                                                    111.6Kbp
                                                                                                                                                                    2741.2Mbp
                                                                                                                                                                    1423.0
                                                                                                                                                                    107.91
                                                                                                                                                                    23.84
                                                                                                                                                                    88.6%
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                                                                                                                                                                    - Number of Contigs - -

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                                                                                                                                                                    This plot shows the number of contigs found for each assembly, broken - down by length.

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                                                                                                                                                                    BUSCO

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                                                                                                                                                                    BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

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                                                                                                                                                                    - - - - - MultiQC v1.9 - - - Written by Phil Ewels, - available on GitHub. -

                                                                                                                                                                    -

                                                                                                                                                                    - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                                                                                          Note that additional data was saved in multiqc_data when this report was generated.

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                                                                                                                                                                          If you use plots from MultiQC in a publication or presentation, please cite:

                                                                                                                                                                          -
                                                                                                                                                                          - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                                          - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                                          - Bioinformatics (2016)
                                                                                                                                                                          - doi: 10.1093/bioinformatics/btw354
                                                                                                                                                                          - PMID: 27312411 -
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                                                                                                                                                                          About MultiQC

                                                                                                                                                                          -

                                                                                                                                                                          This report was generated using MultiQC, version 1.9

                                                                                                                                                                          -

                                                                                                                                                                          You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

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                                                                                                                                                                          For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

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                                                                                                                                                                          You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

                                                                                                                                                                          -

                                                                                                                                                                          MultiQC is published in Bioinformatics:

                                                                                                                                                                          -
                                                                                                                                                                          - MultiQC: Summarize analysis results for multiple tools and samples in a single report
                                                                                                                                                                          - Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
                                                                                                                                                                          - Bioinformatics (2016)
                                                                                                                                                                          - doi: 10.1093/bioinformatics/btw354
                                                                                                                                                                          - PMID: 27312411 -
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                                                                                                                                                                          - A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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                                                                                                                                                                          -

                                                                                                                                                                          Report - - generated on 2022-03-30, 11:11 - - - based on data in: - - /cbio/projects/008/jess/HUPANrun/QuastMiltiQC/allgenomes/KhoeSan

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                                                                                                                                                                          General Statistics

                                                                                                                                                                          - - - - - - - - - - Showing 32/32 rows and 2/2 columns. - -
                                                                                                                                                                          -
                                                                                                                                                                          - -
                                                                                                                                                                          Sample NameN50 (Kbp)Length (Mbp)
                                                                                                                                                                          KSP062.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2492.7Mbp
                                                                                                                                                                          KSP063.assemble_contigs
                                                                                                                                                                          1.7Kbp
                                                                                                                                                                          2468.8Mbp
                                                                                                                                                                          KSP065.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2506.1Mbp
                                                                                                                                                                          KSP067.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          2444.3Mbp
                                                                                                                                                                          KSP069.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          2503.4Mbp
                                                                                                                                                                          KSP092.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          2517.1Mbp
                                                                                                                                                                          KSP096.assemble_contigs
                                                                                                                                                                          1.7Kbp
                                                                                                                                                                          2445.2Mbp
                                                                                                                                                                          KSP103.assemble_contigs
                                                                                                                                                                          1.8Kbp
                                                                                                                                                                          2383.6Mbp
                                                                                                                                                                          KSP105.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          2400.3Mbp
                                                                                                                                                                          KSP106.assemble_contigs
                                                                                                                                                                          2.1Kbp
                                                                                                                                                                          2456.8Mbp
                                                                                                                                                                          KSP111.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2479.9Mbp
                                                                                                                                                                          KSP116.assemble_contigs
                                                                                                                                                                          2.5Kbp
                                                                                                                                                                          2530.2Mbp
                                                                                                                                                                          KSP124.assemble_contigs
                                                                                                                                                                          1.4Kbp
                                                                                                                                                                          2300.2Mbp
                                                                                                                                                                          KSP134.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2508.1Mbp
                                                                                                                                                                          KSP137.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          2477.1Mbp
                                                                                                                                                                          KSP139.assemble_contigs
                                                                                                                                                                          2.6Kbp
                                                                                                                                                                          2549.4Mbp
                                                                                                                                                                          KSP140.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          2525.9Mbp
                                                                                                                                                                          KSP146.assemble_contigs
                                                                                                                                                                          2.5Kbp
                                                                                                                                                                          2528.9Mbp
                                                                                                                                                                          KSP150.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2513.6Mbp
                                                                                                                                                                          KSP152.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          2528.4Mbp
                                                                                                                                                                          KSP154.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          2533.6Mbp
                                                                                                                                                                          KSP155.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          2530.8Mbp
                                                                                                                                                                          KSP224.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          2554.3Mbp
                                                                                                                                                                          KSP225.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          2544.6Mbp
                                                                                                                                                                          KSP228.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          2534.6Mbp
                                                                                                                                                                          LP6005441_DNA_A11.assemble_contigs
                                                                                                                                                                          0.9Kbp
                                                                                                                                                                          1568.7Mbp
                                                                                                                                                                          LP6005441_DNA_B11.assemble_contigs
                                                                                                                                                                          0.8Kbp
                                                                                                                                                                          1367.4Mbp
                                                                                                                                                                          LP6005443_DNA_G08.assemble_contigs
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          2150.8Mbp
                                                                                                                                                                          LP6005592_DNA_C05.assemble_contigs
                                                                                                                                                                          1.4Kbp
                                                                                                                                                                          2324.5Mbp
                                                                                                                                                                          LP6005677_DNA_D03.assemble_contigs
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          2239.1Mbp
                                                                                                                                                                          SAMEA2580840.assemble_contigs
                                                                                                                                                                          5.2Kbp
                                                                                                                                                                          2698.9Mbp
                                                                                                                                                                          SAMEA2580841.assemble_contigs
                                                                                                                                                                          8.5Kbp
                                                                                                                                                                          2735.1Mbp
                                                                                                                                                                          - - -
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                                                                                                                                                                          QUAST

                                                                                                                                                                          -

                                                                                                                                                                          QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

                                                                                                                                                                          - - - - -
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                                                                                                                                                                          - Assembly Statistics - -

                                                                                                                                                                          - - - - -
                                                                                                                                                                          - - - - - - - - - Showing 32/32 rows and 10/10 columns. - -
                                                                                                                                                                          -
                                                                                                                                                                          - -
                                                                                                                                                                          Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
                                                                                                                                                                          KSP062.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          320.5K
                                                                                                                                                                          705777.0K
                                                                                                                                                                          39.5Kbp
                                                                                                                                                                          2492.7Mbp
                                                                                                                                                                          2376.0
                                                                                                                                                                          108.32
                                                                                                                                                                          17.11
                                                                                                                                                                          79.9%
                                                                                                                                                                          KSP063.assemble_contigs
                                                                                                                                                                          1.7Kbp
                                                                                                                                                                          1.0Kbp
                                                                                                                                                                          444.6K
                                                                                                                                                                          927421.0K
                                                                                                                                                                          34.2Kbp
                                                                                                                                                                          2468.8Mbp
                                                                                                                                                                          10666.0
                                                                                                                                                                          108.06
                                                                                                                                                                          17.49
                                                                                                                                                                          78.6%
                                                                                                                                                                          KSP065.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          316.2K
                                                                                                                                                                          693311.0K
                                                                                                                                                                          46.7Kbp
                                                                                                                                                                          2506.1Mbp
                                                                                                                                                                          2587.0
                                                                                                                                                                          106.93
                                                                                                                                                                          17.04
                                                                                                                                                                          80.3%
                                                                                                                                                                          KSP067.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          1.1Kbp
                                                                                                                                                                          351.5K
                                                                                                                                                                          768475.0K
                                                                                                                                                                          42.8Kbp
                                                                                                                                                                          2444.3Mbp
                                                                                                                                                                          2189.0
                                                                                                                                                                          105.76
                                                                                                                                                                          17.07
                                                                                                                                                                          78.3%
                                                                                                                                                                          KSP069.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          309.7K
                                                                                                                                                                          687681.0K
                                                                                                                                                                          42.5Kbp
                                                                                                                                                                          2503.4Mbp
                                                                                                                                                                          2061.0
                                                                                                                                                                          108.16
                                                                                                                                                                          17.27
                                                                                                                                                                          80.3%
                                                                                                                                                                          KSP092.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          316.3K
                                                                                                                                                                          692162.0K
                                                                                                                                                                          39.0Kbp
                                                                                                                                                                          2517.1Mbp
                                                                                                                                                                          2560.0
                                                                                                                                                                          107.87
                                                                                                                                                                          17.37
                                                                                                                                                                          80.7%
                                                                                                                                                                          KSP096.assemble_contigs
                                                                                                                                                                          1.7Kbp
                                                                                                                                                                          1.0Kbp
                                                                                                                                                                          419.9K
                                                                                                                                                                          884356.0K
                                                                                                                                                                          26.8Kbp
                                                                                                                                                                          2445.2Mbp
                                                                                                                                                                          7358.0
                                                                                                                                                                          106.03
                                                                                                                                                                          17.17
                                                                                                                                                                          78.0%
                                                                                                                                                                          KSP103.assemble_contigs
                                                                                                                                                                          1.8Kbp
                                                                                                                                                                          1.1Kbp
                                                                                                                                                                          383.6K
                                                                                                                                                                          817438.0K
                                                                                                                                                                          25.9Kbp
                                                                                                                                                                          2383.6Mbp
                                                                                                                                                                          6297.0
                                                                                                                                                                          108.18
                                                                                                                                                                          17.43
                                                                                                                                                                          76.1%
                                                                                                                                                                          KSP105.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          1.1Kbp
                                                                                                                                                                          340.8K
                                                                                                                                                                          751339.0K
                                                                                                                                                                          41.0Kbp
                                                                                                                                                                          2400.3Mbp
                                                                                                                                                                          2763.0
                                                                                                                                                                          107.78
                                                                                                                                                                          17.19
                                                                                                                                                                          76.9%
                                                                                                                                                                          KSP106.assemble_contigs
                                                                                                                                                                          2.1Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          335.5K
                                                                                                                                                                          731415.0K
                                                                                                                                                                          32.0Kbp
                                                                                                                                                                          2456.8Mbp
                                                                                                                                                                          3772.0
                                                                                                                                                                          109.42
                                                                                                                                                                          17.17
                                                                                                                                                                          78.7%
                                                                                                                                                                          KSP111.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          307.0K
                                                                                                                                                                          685890.0K
                                                                                                                                                                          41.6Kbp
                                                                                                                                                                          2479.9Mbp
                                                                                                                                                                          2332.0
                                                                                                                                                                          109.41
                                                                                                                                                                          17.40
                                                                                                                                                                          79.6%
                                                                                                                                                                          KSP116.assemble_contigs
                                                                                                                                                                          2.5Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          279.9K
                                                                                                                                                                          628835.0K
                                                                                                                                                                          59.0Kbp
                                                                                                                                                                          2530.2Mbp
                                                                                                                                                                          2030.0
                                                                                                                                                                          110.40
                                                                                                                                                                          17.36
                                                                                                                                                                          81.3%
                                                                                                                                                                          KSP124.assemble_contigs
                                                                                                                                                                          1.4Kbp
                                                                                                                                                                          0.9Kbp
                                                                                                                                                                          511.8K
                                                                                                                                                                          1040794.0K
                                                                                                                                                                          27.0Kbp
                                                                                                                                                                          2300.2Mbp
                                                                                                                                                                          21513.0
                                                                                                                                                                          103.22
                                                                                                                                                                          16.55
                                                                                                                                                                          73.0%
                                                                                                                                                                          KSP134.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          318.1K
                                                                                                                                                                          697214.0K
                                                                                                                                                                          40.7Kbp
                                                                                                                                                                          2508.1Mbp
                                                                                                                                                                          2803.0
                                                                                                                                                                          105.88
                                                                                                                                                                          16.68
                                                                                                                                                                          80.4%
                                                                                                                                                                          KSP137.assemble_contigs
                                                                                                                                                                          2.0Kbp
                                                                                                                                                                          1.1Kbp
                                                                                                                                                                          351.4K
                                                                                                                                                                          762298.0K
                                                                                                                                                                          41.3Kbp
                                                                                                                                                                          2477.1Mbp
                                                                                                                                                                          3703.0
                                                                                                                                                                          104.93
                                                                                                                                                                          16.79
                                                                                                                                                                          79.3%
                                                                                                                                                                          KSP139.assemble_contigs
                                                                                                                                                                          2.6Kbp
                                                                                                                                                                          1.4Kbp
                                                                                                                                                                          270.6K
                                                                                                                                                                          609036.0K
                                                                                                                                                                          49.9Kbp
                                                                                                                                                                          2549.4Mbp
                                                                                                                                                                          1908.0
                                                                                                                                                                          107.40
                                                                                                                                                                          17.14
                                                                                                                                                                          82.0%
                                                                                                                                                                          KSP140.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          290.7K
                                                                                                                                                                          649068.0K
                                                                                                                                                                          44.7Kbp
                                                                                                                                                                          2525.9Mbp
                                                                                                                                                                          2058.0
                                                                                                                                                                          106.49
                                                                                                                                                                          16.81
                                                                                                                                                                          81.1%
                                                                                                                                                                          KSP146.assemble_contigs
                                                                                                                                                                          2.5Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          283.6K
                                                                                                                                                                          634573.0K
                                                                                                                                                                          48.4Kbp
                                                                                                                                                                          2528.9Mbp
                                                                                                                                                                          1879.0
                                                                                                                                                                          107.57
                                                                                                                                                                          16.96
                                                                                                                                                                          81.3%
                                                                                                                                                                          KSP150.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          313.4K
                                                                                                                                                                          698336.0K
                                                                                                                                                                          175.9Kbp
                                                                                                                                                                          2513.6Mbp
                                                                                                                                                                          2477.0
                                                                                                                                                                          106.99
                                                                                                                                                                          17.16
                                                                                                                                                                          79.9%
                                                                                                                                                                          KSP152.assemble_contigs
                                                                                                                                                                          2.2Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          324.0K
                                                                                                                                                                          710087.0K
                                                                                                                                                                          38.7Kbp
                                                                                                                                                                          2528.4Mbp
                                                                                                                                                                          2808.0
                                                                                                                                                                          107.26
                                                                                                                                                                          17.24
                                                                                                                                                                          81.0%
                                                                                                                                                                          KSP154.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          302.9K
                                                                                                                                                                          675867.0K
                                                                                                                                                                          57.5Kbp
                                                                                                                                                                          2533.6Mbp
                                                                                                                                                                          2517.0
                                                                                                                                                                          107.69
                                                                                                                                                                          17.18
                                                                                                                                                                          81.1%
                                                                                                                                                                          KSP155.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          310.8K
                                                                                                                                                                          686260.0K
                                                                                                                                                                          41.8Kbp
                                                                                                                                                                          2530.8Mbp
                                                                                                                                                                          2475.0
                                                                                                                                                                          107.36
                                                                                                                                                                          17.29
                                                                                                                                                                          81.1%
                                                                                                                                                                          KSP224.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          300.7K
                                                                                                                                                                          661178.0K
                                                                                                                                                                          63.9Kbp
                                                                                                                                                                          2554.3Mbp
                                                                                                                                                                          1794.0
                                                                                                                                                                          108.13
                                                                                                                                                                          17.27
                                                                                                                                                                          81.9%
                                                                                                                                                                          KSP225.assemble_contigs
                                                                                                                                                                          2.4Kbp
                                                                                                                                                                          1.3Kbp
                                                                                                                                                                          294.4K
                                                                                                                                                                          650219.0K
                                                                                                                                                                          53.0Kbp
                                                                                                                                                                          2544.6Mbp
                                                                                                                                                                          1698.0
                                                                                                                                                                          108.47
                                                                                                                                                                          17.25
                                                                                                                                                                          81.7%
                                                                                                                                                                          KSP228.assemble_contigs
                                                                                                                                                                          2.3Kbp
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          316.0K
                                                                                                                                                                          696109.0K
                                                                                                                                                                          46.1Kbp
                                                                                                                                                                          2534.6Mbp
                                                                                                                                                                          1965.0
                                                                                                                                                                          106.59
                                                                                                                                                                          17.39
                                                                                                                                                                          81.2%
                                                                                                                                                                          LP6005441_DNA_A11.assemble_contigs
                                                                                                                                                                          0.9Kbp
                                                                                                                                                                          0.7Kbp
                                                                                                                                                                          625.2K
                                                                                                                                                                          1148198.0K
                                                                                                                                                                          13.3Kbp
                                                                                                                                                                          1568.7Mbp
                                                                                                                                                                          661.0
                                                                                                                                                                          87.31
                                                                                                                                                                          12.99
                                                                                                                                                                          50.3%
                                                                                                                                                                          LP6005441_DNA_B11.assemble_contigs
                                                                                                                                                                          0.8Kbp
                                                                                                                                                                          0.6Kbp
                                                                                                                                                                          607.0K
                                                                                                                                                                          1091469.0K
                                                                                                                                                                          11.3Kbp
                                                                                                                                                                          1367.4Mbp
                                                                                                                                                                          577.0
                                                                                                                                                                          85.87
                                                                                                                                                                          12.66
                                                                                                                                                                          43.9%
                                                                                                                                                                          LP6005443_DNA_G08.assemble_contigs
                                                                                                                                                                          1.2Kbp
                                                                                                                                                                          0.8Kbp
                                                                                                                                                                          535.2K
                                                                                                                                                                          1076745.0K
                                                                                                                                                                          30.3Kbp
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                                                                                                                                                                          LP6005677_DNA_D03.assemble_contigs
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                                                                                                                                                                          - - - - - MultiQC v1.9 - - - Written by Phil Ewels, - available on GitHub. -

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                                                                                                                                                                          - This report uses HighCharts, - jQuery, - jQuery UI, - Bootstrap, - FileSaver.js and - clipboard.js. -

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                                                                                                                                                                          - - - - - - - - - - - - - - From 3b52fca1956cc1168fa37eb53d45ffb72afdef1e Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Thu, 19 May 2022 10:46:57 +0200 Subject: [PATCH 21/28] Corrected ref genome file name --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b2c0109..94400d2 100644 --- a/README.md +++ b/README.md @@ -112,7 +112,7 @@ Notes: * The trimming and quality control checking of the fastq files for each sample was performed separately to the pipeline. * For most steps, the number of threads used can be specified with the `-t` flag. I usually utilised 8 or 16, depending on the state of the cluster. * Before starting the pipeline, I created a `HUPANdatabases` directory that contains all the necessary databases and reference sequences and annotations needed for the pipeline. In this directory there is: - * The human reference genome fasta file saved in `ref/ref.fa` (downloaded from https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19) + * The human reference genome fasta file saved in `ref/ref.genome.fa` (downloaded from https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19) * The human reference genome transcript file saved in `ref/ref.transcripts.fa` (downloaded from https://www.gencodegenes.org/human/releases.html, release 35) * The human reference genome annotation GTF file saved in `ref/ref.genes.gtf` (downloaded from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.chr_patch_hapl_scaff.annotation.gtf.gz, release 38) * NCBI's BLAST non-redundant nucleotide database saved as `/blastindex/data/blastdb.nal`, downloaded and set up as follows: @@ -141,7 +141,7 @@ This step has been changed from the original HUPAN process; a Nextflow pipeline * The aligned sequences are saved in a folder called `02_aligned`. * `/cbio/bin` is the path to the MUMmer, nucmer and show-cords executable files, which all run through a MUMmer Singularity container. ``` -hupanSLURM alignContig -t 16 01_assembled 02_aligned /cbio/bin /cbio/projects/015/HUPANdatabases/ref/ref.fa +hupanSLURM alignContig -t 16 01_assembled 02_aligned /cbio/bin /cbio/projects/015/HUPANdatabases/ref/ref.genome.fa ``` * This will result in `.delta` and `.coords` files for each sample. * hupanSLURM alignContig code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANrmHighSLURM.pm` @@ -164,7 +164,7 @@ hupanSLURM extractSeq 01_assembled 03_candidate 02_aligned * The QUAST results of the candidate contigs are saved in a folder called `04_quastresult`. * `/cbio/projects/015/HUPANdatabases/images/` is where the QUAST exectuable is located, which runs a QUAST Singularity container. ``` -hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HUPANdatabases/images/ /cbio/projects/015/HUPANdatabases/ref/ref.fa +hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HUPANdatabases/images/ /cbio/projects/015/HUPANdatabases/ref/ref.genome.fa ``` hupanSLURM assemSta code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANassemStaSLURM.pm` @@ -312,7 +312,7 @@ hupanSLURM mergeNovGene 14_genepred/result/ 15_genepredmerge /cbio/bin * This step filters and refines the novel predicted genes based on HUPAN specifications. These specifications can be found in the HUPAN paper supplementary methods. * The first command copies the `non-redundant.fa` sequence file from `12_finalpangenome` to the `15_genepredmerge` directory, because the script needs it to work. Call it `novel.fa`. -* The `ref/` directory contains exactly what the HUPAN script looks for with the exact names, i.e. `ref.fa` and `ref.transcripts.fa` (explained above). +* The `ref/` directory contains exactly what the HUPAN script looks for with the exact names, i.e. `ref.genome.fa` and `ref.transcripts.fa` (explained above). * The last three inputs are (in order) the locations of the BLAST, CD-HIT and RepeatMasker executables respectively. ``` cp 12_finalpangenome/non-redundant.fa 15_genepredmerge/novel.fa @@ -352,7 +352,7 @@ mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primary * `18_map2pan` is the output directory. * `/cbio/projects/015/HUPANdatabases/images/` is where I have stored the Bowtie 2 Singularity container. ``` -cat /cbio/projects/015/HUPANdatabases/ref/ref.fa 12_finalpangenome/non-redundant.fa > 17_pan/pan.fa +cat /cbio/projects/015/HUPANdatabases/ref/ref.genome.fa 12_finalpangenome/non-redundant.fa > 17_pan/pan.fa cd 17_pan && /cbio/projects/015/HUPANdatabases/images/bowtie2-build pan.fa pan && cd .. hupanSLURM alignRead -f bowtie2 -t 8 -s .fastq.gz -k _R 00_fastq 18_map2pan /cbio/projects/015/HUPANdatabases/images/ 17_pan/pan ``` From 867d7aa4d7497e09439cfa3c07677126d221968c Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Tue, 31 May 2022 14:14:39 +0200 Subject: [PATCH 22/28] Added step to fix Quast output --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 94400d2..7bbb997 100644 --- a/README.md +++ b/README.md @@ -168,6 +168,14 @@ hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HU ``` hupanSLURM assemSta code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANassemStaSLURM.pm` +Once this fourth step is finished running, the output needs to be changed slightly (due to the change in aligner in the later QUAST version). +This can be performed using the `fixQuastOutput.py` script located in `/cbio/projects/015/HUPANdatabases/`. +Run this script using the command below and follow the prompts to input the working directory and the population directories. +This step is run interactively and produces output in real time, so first run `screen` and then use an interactive node: `srun --nodes=1 --ntasks=1 -t 6:00:00 --pty bash` +``` +python /cbio/projects/015/HUPANdatabases/fixQuastOutput.py +``` + **(5) Collecting unaligned (both fully and partially) contigs** * This steps collects all unaligned (both fully and partially) contigs from the 03_candidate folder using information from the `04_quastresult` folder. From 6fc316a06e8118703b6736ed57cc249d82b5093f Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Wed, 1 Jun 2022 12:46:52 +0200 Subject: [PATCH 23/28] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 7bbb997..0ef075c 100644 --- a/README.md +++ b/README.md @@ -168,10 +168,10 @@ hupanSLURM assemSta -t 16 03_candidate/data 04_quastresult /cbio/projects/015/HU ``` hupanSLURM assemSta code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANassemStaSLURM.pm` -Once this fourth step is finished running, the output needs to be changed slightly (due to the change in aligner in the later QUAST version). -This can be performed using the `fixQuastOutput.py` script located in `/cbio/projects/015/HUPANdatabases/`. -Run this script using the command below and follow the prompts to input the working directory and the population directories. -This step is run interactively and produces output in real time, so first run `screen` and then use an interactive node: `srun --nodes=1 --ntasks=1 -t 6:00:00 --pty bash` +* Once this fourth step is finished running, the output needs to be changed slightly (due to the change in aligner in the later QUAST version). +* This can be performed using the `fixQuastOutput.py` script located in `/cbio/projects/015/HUPANdatabases/`. +* Run this script using the command below and follow the prompts to input the working directory and the population directory names in that working directory. +* This step is run interactively and produces output in real time, so first run `screen` and then use an interactive node: `srun --nodes=1 --ntasks=1 -t 6:00:00 --pty bash` ``` python /cbio/projects/015/HUPANdatabases/fixQuastOutput.py ``` From 6344cdde23408964e4f7ec0a41b43d0e2faf37da Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Fri, 3 Jun 2022 15:32:41 +0200 Subject: [PATCH 24/28] Update README.md --- README.md | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 0ef075c..aa66c23 100644 --- a/README.md +++ b/README.md @@ -330,24 +330,23 @@ hupanSLURM filterNovGene -t 16 15_genepredmerge 16_genepredfilter /cbio/projects **(17) Assembling the pan-genome** -* This step has does two things. First: - * It takes in the human reference annotation file in `ref/ref.genes.fa` and retains only the longest transcript of each annotation while discarding others, like mRNA, lncRNA, etc. - * The `-f` flag just tells the script that the file is in gtf format, not gff. - * It saves the annotations in a file called `ref.genes-ptpg.gtf`, found in the `/cbio/projects/015/HUPANdatabases/ref` directory. - * The annotation file was downloaded from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.chr_patch_hapl_scaff.annotation.gtf.gz (release 38). +* This step has does multiple things. First: + * It takes in the human reference annotation file in `ref/ref.genes.fa` and retains only the longest transcript of each annotation while discarding others, like mRNA, lncRNA, etc. It also removes any annotations from patch/alt/decoy/unplaced/mitochondrial DNA contigs, as the HUPAN pipeline seems to be unable to recognise them. + * This step, however, HAS ALREADY BEEN COMPLETED using the original HUPAN `pTpG` script and some additional scripting to remove the extra annotations.The primary annotations have been saved in a file called ` ref.genes-ptpg-primaryseqs.gtf`, found in the `/cbio/projects/015/HUPANdatabases/ref` directory. + * NO MORE ACTION IS REQUIRED FOR THIS ANNOTATIOIN FILE. You can use it as is. Should a new annotation file need to be made, contact Jess Bourn for guidance. + * Some additional information: + * The original annotation file was downloaded from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.chr_patch_hapl_scaff.annotation.gtf.gz (release 38). * The annotation file downloaded MUST be later than release 21, otherwise the HUPAN script won't work as it will be in a different format (format changed after release 21). - * However, you also have to remove any annotations from patch/alt/decoy/unplaced/mitochondrial DNA contigs, as the HUPAN pipeline seems to be unable to recognise them. So remove from the annotation file all lines after "chrY" annotations. I have not shown this step below, as the exact line numbers may be different. - * In summary: run the `pTpG` script on the annotation file, and then remove the extra annotations and save the final working file as `ref.genes-ptpg-primaryseqs.gtf`. -* Then secondly, we combine this annotation file and the novel sequence annotation (from step 16) into one annotation file - * You must first convert the novel annotation file into GTF format too, or otherwise start with GFF format for the reference annotation. -* Both steps done in real time (interactively) so use `screen` and then start an interactive node with extra memory: `srun --mem=15g --pty bash` -``` -hupanSLURM pTpG -f /cbio/projects/015/HUPANdatabases/ref/ref.genes.gtf /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg.gtf -# insert step to remove any additional annotations and save the primary sequence annotations as ref.genes-ptpg-primaryseqs.gtf -# insert step to convert the Final.gff file to GTF format. -mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primaryseqs.gtf 16_genepredfilter/data/Final/Final.gtf > 17_pan/pan.gtf -``` -* hupanSLURM pTpG code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANpTpGSLURM.pm` +* Then secondly, we convert the novel annotation file (GFF format) into GTF format in order to combine it succcessfully with the primary sequence annotation GTF file. + * This is done using an adapted form of the HUPAN `pTpG` script and the result is saved in the same `16_genepredfilter/data/Final/` directory. +* Once these two steps have been completed, the two files can be merged to make the pan-genome annotation file. +* These steps are done in real time (interactively) so use `screen` and then start an interactive node with extra memory: `srun --mem=10g --pty bash` +``` +hupanSLURM pTpG 16_genepredfilter/data/Final/Final.gff 16_genepredfilter/data/Final/Final-ptpg.gtf +mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primaryseqs.gtf 16_genepredfilter/data/Final/Final-ptpg.gtf > 17_pan/pan.gtf +``` +* The original hupanSLURM pTpG code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANpTpGSLURMoriginal.pm` +* The MAKER-adapted hupanSLURM pTpG code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANpTpGSLURM.pm` **(18) Aligning the samples to the pan-genome** From 9fe8a1e5fab06e76afd1b534909a1ceebcd66f8c Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Fri, 3 Jun 2022 15:35:35 +0200 Subject: [PATCH 25/28] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index aa66c23..9831f1f 100644 --- a/README.md +++ b/README.md @@ -330,7 +330,7 @@ hupanSLURM filterNovGene -t 16 15_genepredmerge 16_genepredfilter /cbio/projects **(17) Assembling the pan-genome** -* This step has does multiple things. First: +* This step does multiple things. First: * It takes in the human reference annotation file in `ref/ref.genes.fa` and retains only the longest transcript of each annotation while discarding others, like mRNA, lncRNA, etc. It also removes any annotations from patch/alt/decoy/unplaced/mitochondrial DNA contigs, as the HUPAN pipeline seems to be unable to recognise them. * This step, however, HAS ALREADY BEEN COMPLETED using the original HUPAN `pTpG` script and some additional scripting to remove the extra annotations.The primary annotations have been saved in a file called ` ref.genes-ptpg-primaryseqs.gtf`, found in the `/cbio/projects/015/HUPANdatabases/ref` directory. * NO MORE ACTION IS REQUIRED FOR THIS ANNOTATIOIN FILE. You can use it as is. Should a new annotation file need to be made, contact Jess Bourn for guidance. @@ -340,7 +340,7 @@ hupanSLURM filterNovGene -t 16 15_genepredmerge 16_genepredfilter /cbio/projects * Then secondly, we convert the novel annotation file (GFF format) into GTF format in order to combine it succcessfully with the primary sequence annotation GTF file. * This is done using an adapted form of the HUPAN `pTpG` script and the result is saved in the same `16_genepredfilter/data/Final/` directory. * Once these two steps have been completed, the two files can be merged to make the pan-genome annotation file. -* These steps are done in real time (interactively) so use `screen` and then start an interactive node with extra memory: `srun --mem=10g --pty bash` +* These steps are done in real time (interactively) so use `screen` and then start an interactive node: `srun --pty bash` ``` hupanSLURM pTpG 16_genepredfilter/data/Final/Final.gff 16_genepredfilter/data/Final/Final-ptpg.gtf mkdir 17_pan && cat /cbio/projects/015/HUPANdatabases/ref/ref.genes-ptpg-primaryseqs.gtf 16_genepredfilter/data/Final/Final-ptpg.gtf > 17_pan/pan.gtf From 2fe2df5dfabb0b6affd915889978dfa7e9385e9d Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Fri, 1 Jul 2022 10:21:03 +0200 Subject: [PATCH 26/28] Added details about Y chromosome annotations --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 9831f1f..049fc37 100644 --- a/README.md +++ b/README.md @@ -381,11 +381,15 @@ hupanSLURM sam2bam -t 8 18_map2pan/data 19_panBam /cbio/bin * This step calculates the coverage of each gene or CDS in all of the genomes used. * It does this by looking at the alignment information in the indexed and sorted `.bam` files from the previous step and identifying whether these alignments fall within the annotations in the `pan.gtf` file. -* The results will be output to the `20_geneCov` directory. +* The results will be output to the `20_geneCovwithY` directory. +* Of importnace: the HUPAN authors removed the Y chromosome genes/CDS regions from further analysis as these would be classified as "distributed" in female samples (as they do not have Y chromosome genes). + * We also implemented this using the second command below. + * First, a copy is made of the original directory so the data is available if needed. Then 'sed' is used to remove all annotation lines containing the string 'chrY'. ``` -hupanSLURM geneCov -t 8 19_panBam/data 20_geneCov/ 17_pan/pan.gtf +hupanSLURM geneCov -t 8 19_panBam/data 20_geneCovwithY/ 17_pan/pan.gtf +cp -r 20_geneCovwithY 20_geneCov && cd 20_geneCov/data && for i in *; do sed -i '/chrY/d' $i/$i.sta; done && cd ../../ ``` -* This will result in a `.sta` file for each genome. +* This will result in two `.sta` files for each sample, one containing Y annotations and one not. * hupanSLURM geneCov code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgeneCovSLURM.pm` **(21) Determing gene presence-absence variance profile** From b21dc3b5fe716319ef788c6cab965972e090d1f7 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sat, 2 Jul 2022 11:02:53 +0200 Subject: [PATCH 27/28] Update README.md --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 049fc37..e8b04a5 100644 --- a/README.md +++ b/README.md @@ -382,9 +382,10 @@ hupanSLURM sam2bam -t 8 18_map2pan/data 19_panBam /cbio/bin * This step calculates the coverage of each gene or CDS in all of the genomes used. * It does this by looking at the alignment information in the indexed and sorted `.bam` files from the previous step and identifying whether these alignments fall within the annotations in the `pan.gtf` file. * The results will be output to the `20_geneCovwithY` directory. -* Of importnace: the HUPAN authors removed the Y chromosome genes/CDS regions from further analysis as these would be classified as "distributed" in female samples (as they do not have Y chromosome genes). - * We also implemented this using the second command below. - * First, a copy is made of the original directory so the data is available if needed. Then 'sed' is used to remove all annotation lines containing the string 'chrY'. +* Of importnace: the HUPAN authors removed the Y chromosome genes/CDS regions from further analysis as these would be classified as "distributed" in female samples, even if they are not distributed in male samples. + * We similarly implemented this using the second command below. + * First, a copy is made of the original directory so the Y chromosome presence/absence data is available if required at a later stage. Then, in the new `20_geneCov` directory, 'sed' is used to remove all annotation lines containing the string 'chrY' and the edited files are saved. + * These files lacking Y chromosome data are used in all subsequent steps. ``` hupanSLURM geneCov -t 8 19_panBam/data 20_geneCovwithY/ 17_pan/pan.gtf cp -r 20_geneCovwithY 20_geneCov && cd 20_geneCov/data && for i in *; do sed -i '/chrY/d' $i/$i.sta; done && cd ../../ From 409d4780939a0308f429e7d22e4eabc85f9ff735 Mon Sep 17 00:00:00 2001 From: Jess Bourn <41609937+BournSupremacy@users.noreply.github.com> Date: Sat, 23 Jul 2022 15:28:51 +0200 Subject: [PATCH 28/28] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index e8b04a5..9a13281 100644 --- a/README.md +++ b/README.md @@ -269,13 +269,13 @@ hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/nonrefernce.before.fa 1 **At this point, each population has its own non-redundant non-reference sequences. Now we can combine them and remove redundancy.** **By doing this, we are ending up with the same sequences we would have had if we had run all the populations together, but now we have the population-specific information separated and can easily perform downstream or upstream analysis on population differences.** -* To do this, use `cat` to combine all the sequences into one file, and then use CD-HIT to remove redundancy at 90%. +* To do this, use `cat` to combine all the sequences into one file, and then use CD-HIT to remove redundancy at 95%. * The population directories should all be in the same location and can therefore be accessed using *. * The final non-reference sequences are saved in `allpopulations/` ``` cat */12_finalpangenome/non-redundant.fa > ../allpopulations/11_nonreference/all.nonreference.before.fa cd ../allpopulations -hupanSLURM rmRedundant cdhitCluster -t 8 11_nonreference/all.nonreference.before.fa 12_finalpangenome /cbio/bin/ +hupanSLURM rmRedundant cdhitCluster -t 8 -c 0.95 11_nonreference/all.nonreference.before.fa 12_finalpangenome /cbio/bin/ ``` * This will result in the final non-redundant non-reference sequence file in `allpopulations/12_finalpangenome/non-redundant.fa` for all populations combined. * All steps from this point are performed in the `allpopulations/` directory. @@ -299,7 +299,7 @@ hupanSLURM splitSeq -m 2000000 12_finalpangenome/non-redundant.fa 13_genepredinp * The config is the MAKER configuration file where we have specified all of the variables and datasets to use. A copy of this config file can be found in this repository. * `/cbio/bin` is the location of the MAKER executable, which runs a MAKER Singularity container. ``` -hupanSLURM genePre -t 16 13_genepredinput 14_genepred /cbio/projects/008/jess/HUPANrun/AfricanPanGenome/config /cbio/bin +hupanSLURM genePre -t 16 13_genepredinput 14_genepred /cbio/projects/015/HUPANrun/AfricanPanGenome/RefGraphMAKERconfig /cbio/bin ``` * This will result in various MAKER predictions for each `part*.fa` file. * hupanSLURM genePre code is found in `/cbio/projects/015/HUPANdatabases/HUPAN/lib/HUPANgenePreSLURM.pm`