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.