diff --git a/Readme.txt b/Readme.txt index 74e0f3c..6e7a95c 100755 --- a/Readme.txt +++ b/Readme.txt @@ -24,30 +24,36 @@ The steps to install SURPI on a machine are as follows: The below software must be installed for SURPI to function properly. + • Abyss (v1.3.5) + http://www.bcgsc.ca/platform/bioinfo/software/abyss + • cutadapt (v1.2.1) + https://code.google.com/p/cutadapt/ + • dropcache + http://stackoverflow.com/questions/13646925/allowing-a-non-root-user-to-drop-cache + • fastq + https://github.com/brentp/bio-playground/tree/master/reads-utils • fastQValidator http://genome.sph.umich.edu/wiki/FastQValidator + • fqextract + https://gist.github.com/drio/1168330 + • gt (v1.5.1) + http://genometools.org/index.html • Minimo (v1.6) http://sourceforge.net/projects/amos/files/amos/3.1.0/ - • Abyss (v1.3.5) - http://www.bcgsc.ca/platform/bioinfo/software/abyss + • Open MPI: + https://www.open-mpi.org/ + • Perl DBD::Sqlite: + http://search.cpan.org/~ishigaki/DBD-SQLite-1.50/lib/DBD/SQLite.pm + • pigz + http://www.zlib.net/pigz/ + • prinseq-lite.pl + http://prinseq.sourceforge.net • RAPSearch (v2.12) http://omics.informatics.indiana.edu/mg/RAPSearch2/ • seqtk (v 1.0r31) https://github.com/lh3/seqtk • SNAP (v0.15) http://snap.cs.berkeley.edu - • gt (v1.5.1) - http://genometools.org/index.html - • fastq - https://github.com/brentp/bio-playground/tree/master/reads-utils - • fqextract - https://gist.github.com/drio/1168330 - • cutadapt (v1.2.1) - https://code.google.com/p/cutadapt/ - • prinseq-lite.pl - http://prinseq.sourceforge.net - • dropcache - http://stackoverflow.com/questions/13646925/allowing-a-non-root-user-to-drop-cache 2. Decompress SURPI