'\" t
.\"     Title: gt-shredder
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-SHREDDER" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
gt-shredder \- Shredder sequence file(s) into consecutive pieces of random length\&.
.SH "SYNOPSIS"
.sp
\fBgt shredder\fR [option \&...] [sequence_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-coverage\fR [\fIvalue\fR]
.RS 4
set the number of times the sequence_file is shreddered (default: 1)
.RE
.PP
\fB\-minlength\fR [\fIvalue\fR]
.RS 4
set the minimum length of the shreddered fragments (default: 300)
.RE
.PP
\fB\-maxlength\fR [\fIvalue\fR]
.RS 4
set the maximum length of the shreddered fragments (default: 700)
.RE
.PP
\fB\-overlap\fR [\fIvalue\fR]
.RS 4
set the overlap between consecutive pieces (default: 0)
.RE
.PP
\fB\-sample\fR [\fIvalue\fR]
.RS 4
take samples of the generated sequences pieces with the given probability (default: 1\&.000000)
.RE
.PP
\fB\-clipdesc\fR [\fIyes|no\fR]
.RS 4
clip descriptions after first space (fooled by
\fI\et\fR,
\fI\en\fR
etc) adds offset and length to ensure unique identifier (default: no)
.RE
.PP
\fB\-width\fR [\fIvalue\fR]
.RS 4
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
.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\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
Each sequence given in \fIsequence_file\fR is shreddered into consecutive pieces of random length (between \fI\-minlength\fR and \fI\-maxlength\fR) until it is consumed\&. By this means the last shreddered fragment of a given sequence can be shorter than the argument to option \fI\-minlength\fR\&. To get rid of such fragments use gt seqfilter (see example below)\&.
.SH "EXAMPLES:"
.sp
Shredder a given BAC:
.sp
.if n \{\
.RS 4
.\}
.nf
$ gt shredder U89959_genomic\&.fas > fragments\&.fas
.fi
.if n \{\
.RE
.\}
.sp
Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp:
.sp
.if n \{\
.RS 4
.\}
.nf
$ gt shredder \-minlength 50 \-maxlength 100 U89959_ests\&.fas \e
  | gt seqfilter \-minlength 50 \- > fragments\&.fas
# 130 out of 1260 sequences have been removed (10\&.317%)
.fi
.if n \{\
.RE
.\}
.sp
Shredder an EST collection and show only random 10% of the resulting fragments:
.sp
.if n \{\
.RS 4
.\}
.nf
$ gt shredder \-sample 0\&.1 U89959_ests\&.fas
.fi
.if n \{\
.RE
.\}
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.