'\" t
.\" Title: gt-readjoiner
.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.79.1
.\" Date: 01/06/2017
.\" Manual: GenomeTools Manual
.\" Source: GenomeTools 1.5.9
.\" Language: English
.\"
.TH "GT\-READJOINER" "1" "01/06/2017" "GenomeTools 1\&.5\&.9" "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-readjoiner \- Readjoiner: a string graph\-based sequence assembler\&.
.SH "SYNOPSIS"
.sp
\fBgt readjoiner\fR [option \&...] tool [argument \&...]
.SH "DESCRIPTION"
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
Please consult the Readjoiner manual for more information\&.
.sp
Tools:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fBprefilter\fR
prepare the readset for Readjoiner
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fBoverlap\fR
calculate suffix\-prefix matches
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
\fBassembly\fR
construct string graph and output contigs
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to \&.