.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH KISSNP2 "1" "October 2014" "kissnp2 1.2.5" "User Commands"
.SH NAME
kissnp2 \- manual page for kissnp2 1.2.5
.SH DESCRIPTION
NAME
kissnp, version DiscoSnp \- kissnp submodule 1.2.5 \- Copyright INRIA \- CeCILL License
.PP
SYNOPSIS
kissnp2/kissnp2 <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] \fB\-o\fR name [\-t] [\-e length] [\-l] [\-b] [\-k value] [\-c value] [\-g value] [\-h]
.IP
or:
.PP
kissnp2/kissnp2 input_names_file.txt \fB\-o\fR name [\-t] [\-e length] [\-l] [\-b] [\-k value] [\-c value] [\-g value] [\-h]
.IP
with "input_names_file.txt" being a file containing on each line the name of read files
.PP
DESCRIPTION
.IP
"kissnp2", detects SNPs from read set(s). It should usually be followed by the "kissreads" for recovering coverage and quality information from reads.
.PP
MANDATORY
.IP
At least one read set.
\fB\-o\fR file_name_prefix: where to write outputs and debruijn graph structure files.
.PP
OPTIONS
.HP
\fB\-t\fR extend found and stop at first polymorphism (strict extension=unitigs) SNPs. Uncompatible with \fB\-T\fR
.HP
\fB\-T\fR extend found and stop at large polymorphism (extension=contigs) SNPs. Uncompatible with \fB\-t\fR
.HP
\fB\-e\fR length: extend found SNPs (option \fB\-t\fR) and conserve only those whose min(left and right extension) is bigger or equal to "length"
.HP
\fB\-l\fR conserve low complexity SNPs. Default: false (filter out low complexity results)
.HP
\fB\-b\fR INT:
.TP
0: forbid SNPs for wich any of the two paths is branching (high precision, low recall).
Default value
.IP
1: forbid SNPs for wich the two paths are branching (e.g. the two paths can be created either with a 'A' or a 'C' at the same position
2: No limitation on branching (low precision, high recall)
.HP
\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 27.
.HP
\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
.HP
\fB\-C\fR max_coverage: a sequence is covered by at most max_coverage coherent reads. Default: infiny (=2147483647 on your computer :) )
.HP
\fB\-g\fR estimated_genome_size: estimation of the size of the genome whose reads come from.
.IP
It is in bp, does not need to be accurate, only controls memory usage. Default: 3 billion
.HP
\fB\-h\fR prints this message and exit
.PP
DiscoSnp \- kissnp submodule 1.2.5 \- Copyright INRIA \- CeCILL License
The command line was:
kissnp2/kissnp2 \fB\-h\fR
.SH "SEE ALSO"
The full documentation for
.B kissnp2
is maintained as a Texinfo manual.  If the
.B info
and
.B kissnp2
programs are properly installed at your site, the command
.IP
.B info kissnp2
.PP
should give you access to the complete manual.