NAME

       mapsembler2_kissreads_graph - maps the provided reads on the graph

SYNOPSIS

       mapsembler2_kissreads_graph             input_graph             <readsC1.fasta/fastq[.gz]>
       [<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] -M  -t  type  [-k  value]  [-c
       min_coverage] [-d max_substitutions] [-o name] [-h]

DESCRIPTION

       mapsembler2_kissreads_graph  maps  the  provided  reads  on  the  graph  With  option  "-t
       coverage": outputs an equivalent graph removing uncovered edges and adding:

              for each node: the coverage per sample and per position

              for each edge: the number of mapped reads per sample using this edge

       With option "-t modify": outputs the same simplified graph:

              removing low covered edges and nodes (less that min_coverage) then  phasing  simple
              non branching paths

       If  -M option is specified, the input is considered as a Mapsembler output - thus composed
       of multiple independent graphes

OPTIONS

   MANDATORY
       -t <type>

              "c" "coverage"

              "m" "modify"

   OPTIONAL
       -M: the input is considered as a Mapsembler output

       -o file_name: write obtained graph. Default: standard output

       -k size_seed: will use seeds of length size_seed. Default: 25.

       -c min_coverage: Will consider an edge as coherent if coverage (number of reads  from  all
              sets using this edge) is at least min_coverage. Default: 2

       -d  max_substitutions:  Will  map  a  read  on  the  graph  with at most max_substitutions
              substitutions. Default: 1

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.