config.txt

Project name              = Test
Combined reads or ASVs    = /path/to/reads/or/ASVs/ASVs.fasta
Forward reads             = /path/to/reads/reads_1.fastq (at the moment only the ASV option is available)
Reverse reads             = /path/to/reads/reads_2.fastq (at the moment only the ASV option is available)
Keep read ids             = 
Nucleotide database       = /path/to/nucleotide/database/from/NCBI/nt
Taxonomy database         = /path/to/taxanomy/database/from/NCBI/taxonomy.xml
Taxonomy only             = yes
Threads                   = 4
Output path               = /path/to/output/folder/

#Project name              = Choose a name for your project, it will be used for the output files.
#Combined reads or ASVs    = /home/nicolas/Perl/OIST/eDNA/Michael/NC_asv_table.fasta
#Forward reads             = The path to the file that contains the forward reads (not necessary when there is a Combined or ASV file)
#Reverse reads             = The path to the file that contains the reverse reads (not necessary when there is a Combined or ASV file)
#Keep read ids             = When yes, the read ids from the fasta or fastq files are used in the output files, otherwise they will be changed to numbers (yes/no)
#Nucleotide database       = /path/to/nucleotide/database/from/NCBI/nt (https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/blast/update_blastdb.pl) (Other databeses with the same structure can also be used)
#Taxonomy database         = /home/nicolas/Perl/OIST/eDNA/taxonomy.xml (http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/taxonomy.xml.gz)
#Taxonomy only             = When yes, ASVs will directly be used for taxonomy assignment without prior clustering. (yes/no)ù
#Threads                   = Increasing the number of cores will speed up the runtime.
#Output path               = You can change the directory where all the output files wil be stored.