.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH MAPSEMBLER2_KISSREADS_GRAPH "1" "October 2018" "mapsembler2_kissreads_graph 2.2.4" "User Commands"
.SH NAME
mapsembler2_kissreads_graph \- maps the provided reads on the graph
.SH SYNOPSIS
.B 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]
.SH DESCRIPTION
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
.IP
for each edge: the number of mapped reads per sample using this edge
.P
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 independent graphes
.SH OPTIONS
.SS MANDATORY
.HP
\fB\-t\fR <type>
.IP
"c" "coverage"
.IP
"m" "modify"
.SS OPTIONAL
\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 AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.