'\" t
.\"     Title: gt-simreads
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-SIMREADS" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-simreads \- Simulate sequencing reads from random positions in the input sequence(s)\&.
.SH "SYNOPSIS"
.sp
\fBgt simreads\fR [option \&...] <encseq>
.SH "DESCRIPTION"
.PP
\fB\-num\fR [\fIvalue\fR]
.RS 4
desired number of reads (default: undefined)
.RE
.PP
\fB\-coverage\fR [\fIvalue\fR]
.RS 4
desired coverage of the reads (default: undefined)
.RE
.PP
\fB\-len\fR [\fIvalue\fR]
.RS 4
fixed read length (default: undefined)
.RE
.PP
\fB\-minlen\fR [\fIvalue\fR]
.RS 4
minimal read length (default: undefined)
.RE
.PP
\fB\-maxlen\fR [\fIvalue\fR]
.RS 4
maximal read length (default: undefined)
.RE
.PP
\fB\-distlen\fR [\fIstring\fR]
.RS 4
use read length distribution file (in the output format of the seqstat tool) (default: undefined)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-p\fR [\fIyes|no\fR]
.RS 4
show a progress bar (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-ds\fR [\fIstring\fR]
.RS 4
output distribution of starting positions to specified file (default: undefined)
.RE
.PP
\fB\-dl\fR [\fIstring\fR]
.RS 4
output distribution of read lengths to specified file (default: undefined)
.RE
.PP
\fB\-ss\fR [\fIyes|no\fR]
.RS 4
simulate reads in forward direction only (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help for basic options and exit
.RE
.PP
\fB\-help+\fR
.RS 4
display help for all options and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to <gonnella@zbh\&.uni\-hamburg\&.de>\&.