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.