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.

mapsembler2_kissreads_graph 2.2.4+dfsg           September 2017                   MAPSEMBLER2_KISSREADS_GRAPH(1)