.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KISSREADS2 "1" "January 2019" "kissreads2 2.3.0" "User Commands"
.SH NAME
kissreads2 \- enhances the kissnp2 results by computing per read set
.SH DESCRIPTION
[Kissreads2 options]
.TP
\fB\-x\fR
(0 arg) :    radseq option, homogeneous read depth along the prediction
.TP
\fB\-predictions\fR
(1 arg) :    Input predictions
.TP
\fB\-reads\fR
(1 arg) :    Input reads
.TP
\fB\-unco\fR
(1 arg) :    Output uncoherent file name  [default '/dev/null']
.TP
\fB\-co\fR
(1 arg) :    Output coherent file name
.TP
\fB\-hamming\fR
(1 arg) :    Maximal hamming distance authorized while maping  [default '1']
.TP
\fB\-coverage_file\fR (1 arg) :
File (.h5) generated by kissnp2, containing the coverage threshold per read set  [default '_removemeplease']
.TP
\fB\-k\fR
(1 arg) :    Size of k, used as minial overlap and kmer spanning read coherence  [default '31']
.TP
\fB\-index_stride\fR
(1 arg) :    Index Stride  [default '2']
.TP
\fB\-size_seeds\fR
(1 arg) :    Size of the used seeds (distinct from the size of k)  [default '25']
.TP
\fB\-output_fasta\fR
(0 arg) :    Output standard Fasta. By default the output is formatted especially for the discoSnp++ pipeline
.TP
\fB\-genotype\fR
(0 arg) :    Compute genotypes
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores  [default '0']
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-version\fR
(0 arg) :    version
.TP
\fB\-help\fR
(0 arg) :    help
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.