.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.7.
.TH MAPSEMBLER2_EXTREMITIES "1" "October 2018" "mapsembler2_extremities 2.2.4" "User Commands"
.SH NAME
mapsembler2_extremities \- performs the first step of Mapsembler2_extend
.SH SYNOPSIS
.B mapsembler2_extremities
\fB\-\-k\fR <kmersize> \fB\-\-starters\fR <fasta> \fB\-\-reads\fR <dataset> \fB\-\-output\fR <substarterfile> [optional arguments]
.SH DESCRIPTION
This modules performs the first step of Mapsembler2_extend. For each starter, it outputs a list of extremities of the starter (of length *k*) are found in the reads, up to 1 indel or mismatch.
.SH OPTIONS
.TP
\fB\-\-k\fR (1 arg):
kmer size that will be used for mapsembler2  [default '']
.TP
\fB\-\-starters\fR (1 arg):
starters fasta file  [default '']
.TP
\fB\-\-reads\fR(1 arg):
reads dataset file name. Several reads sets can be provided, surrounded by "'s and separated by a space (e.g. \fB\-\-reads\fR "reads1.fa reads2.fa")  [default '']
.TP
\fB\-\-output\fR (1 arg):
output substarters file name  [default '']
.TP
\fB\-\-min\-solid\-subkmer\fR (1 arg):
minimim abundance to keep a subkmer  [default '3']
.TP
\fB\-debug\fR (0 arg):
debugging
.TP
\fB\-nb\-cores\fR (1 arg):
number of cores  [default '0']
.TP
\fB\-verbose\fR (1 arg):
verbosity level  [default '1']
.TP
\fB\-help\fR (0 arg):
display help about possible options
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.