NAME

       run_mapsembler2_pipeline - manual page for run_mapsembler2_pipeline 2.2.4+dfsg

SYNOPSIS

       run_mapsembler_and_phaser.sh -s <starter.fasta> -r <reads.faste> -t [1/2/3/4]<options>

DESCRIPTION

       run_mapsembler_pipeline.sh,  a  pipelining mapsembler2_extremities, mapsembler2_extend and
       kissread_g

              -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=contig(graph)

   <options>:
              -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. Default=5. Example -c 5 -d value.
              Set  the number of authorized substitutions used while mapping reads on found SNPs.
              Default=1. Example: -d 1 -g value. Estimated genome  size.  Used  only  to  control
              memory  usage.  e.g.  3  billion  (3000000000) uses 4Gb of RAM. Default=10 million.
              Example: -d 10000000 -f value. Set the process of search in  the  graph  (1=Breadth
              and  2=Depth).  Default=1.  Example:  -f 1 -x value. Set the maximal nodes length .
              Default=40. Example: -x 40 -y value. Set the maximal graph depth  .  Default=10000.
              Example: -y 10000 -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_mapsembler2_pipeline is maintained as a Texinfo manual.  If
       the info and run_mapsembler2_pipeline programs are properly installed at  your  site,  the
       command

              info run_mapsembler2_pipeline

       should give you access to the complete manual.