NAME

       mapsembler2_kissreads_graph - manual page for mapsembler2_kissreads_graph 2.2.4+dfsg

DESCRIPTION

       NAME ./kissreads_graph/mapsembler2_kissreads_graph, version 1.0.0 Beta - Copyright INRIA -
       CeCILL License

       -h prints this message and exit

       USAGE ./kissreads_graph/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 ./kissreads_graph/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 independant graphes

       MANDATORY

       -t <type>

              "c" "coverage" "m" "modify"

       OPTIONS -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

SEE ALSO

       The  full documentation for mapsembler2_kissreads_graph is maintained as a Texinfo manual.
       If the info and mapsembler2_kissreads_graph programs are properly installed at your  site,
       the command

              info mapsembler2_kissreads_graph

       should give you access to the complete manual.