.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH MAPSEMBLER2_KISSREADS_GRAPH "1" "September 2016" "mapsembler2_kissreads_graph 2.2.3+dfsg" "User Commands"
.SH NAME
mapsembler2_kissreads_graph \- manual page for mapsembler2_kissreads_graph 2.2.3+dfsg
.SH DESCRIPTION
NAME
\&./kissreads_graph/mapsembler2_kissreads_graph, version 1.0.0 Beta \- Copyright INRIA \- CeCILL License
.HP
\fB\-h\fR prints this message and exit
.PP
USAGE
\&./kissreads_graph/mapsembler2_kissreads_graph input_graph <readsC1.fasta/fastq[.gz]> [<readsC2.fasta/fastq[.gz]> [<readsC3.fasta/fastq[.gz] ...] \fB\-M\fR \fB\-t\fR type [\-k value] [\-c min_coverage] [\-d max_substitutions] [\-o name] [\-h]
.PP
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:
.IP
for each node: the coverage per sample and per position
for each edge: the number of mapped reads per sample using this edge
.SS "With option "-t modify": outputs the same simplified graph:"
.IP
removing low covered edges and nodes (less that min_coverage)
then phasing simple non branching paths
.PP
If \fB\-M\fR option is specified, the input is considered as a Mapsembler output \- thus composed of multiple independant graphes
.PP
MANDATORY
.HP
\fB\-t\fR <type>
.IP
"c" "coverage"
"m" "modify"
.PP
OPTIONS
\fB\-M\fR: the input is considered as a Mapsembler output
.HP
\fB\-o\fR file_name: write obtained graph. Default: standard output
.HP
\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.
.HP
\fB\-c\fR 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
.HP
\fB\-d\fR max_substitutions: Will map a read on the graph with at most max_substitutions substitutions. Default: 1
.SH "SEE ALSO"
The full documentation for
.B mapsembler2_kissreads_graph
is maintained as a Texinfo manual.  If the
.B info
and
.B mapsembler2_kissreads_graph
programs are properly installed at your site, the command
.IP
.B info mapsembler2_kissreads_graph
.PP
should give you access to the complete manual.