NAME

       run_mapsembler_and_phaser - manual page for run_mapsembler_and_phaser 2.0.5+dfsg

SYNOPSIS

       run_read2SNPs.sh OPT

DESCRIPTION

       run_read2SNPs.sh,  a pipelining kissnp2 and kissreads for calling SNPs from NGS reads without the need of
       a reference genome

              OPT:

              -s: file containing starters (fasta) -r list of reads separated by space, surrounded  by  the  '"'
              character.  Note  that  reads  may  be  in  fasta  or  fastq  format,  gzipped or not. Example: -r
              "data_sample/reads_sequence1.fasta   data_sample/reads_sequence2.fasta.gz".  -t: kind of assembly:
              1=unitig  (fasta),  2=contig  (fasta),  3=unitig (graph), 4=unitig(graph) -p prefix. All out files
              will start with this prefix. Example: -p my_prefix -k value. Set the length of  used  kmers.  Must
              fit  the  compiled  value.  Default=31.  Example -k 31 -c value. Set the minimal coverage: Used by
              kissnp2 (don't use kmers with lower coverage) and kissreads (read coherency threshold). Default=4.
              Example  -c  4  -d  value.  Set the number of authorized substitutions used while mapping reads on
              found SNPs (kissreads). Default=1. Example: -d 1 -g value. Estimated genome  size.  Used  only  to
              control  kissnp2  memory  usage.  e.g. 3 billion (3000000000) uses 4Gb of RAM. Default=10 million.
              Example: -d 10000000 -h: Prints this message and exist

       Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr

SEE ALSO

       The full documentation for run_mapsembler_and_phaser is maintained as a Texinfo manual.  If the info  and
       run_mapsembler_and_phaser programs are properly installed at your site, the command

              info run_mapsembler_and_phaser

       should give you access to the complete manual.