'\" t
.\"     Title: gt-readjoiner-assembly
.\"    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\-READJOINER\-ASSE" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-readjoiner-assembly \- Construct string graph and output contigs\&.
.SH "SYNOPSIS"
.sp
\fBgt readjoiner assembly\fR [option \&...]
.SH "DESCRIPTION"
.PP
\fB\-readset\fR [\fIstring\fR]
.RS 4
specify the readset name (default: undefined)
.RE
.PP
\fB\-spmfiles\fR [\fIvalue\fR]
.RS 4
number of SPM files to read this must be equal to the value of \-j for the overlap phase (default: 1)
.RE
.PP
\fB\-l\fR [\fIvalue\fR]
.RS 4
specify the minimum SPM length (default: 0)
.RE
.PP
\fB\-depthcutoff\fR [\fIvalue\fR]
.RS 4
specify the minimal number of nodes in a contig (default: 3)
.RE
.PP
\fB\-lengthcutoff\fR [\fIvalue\fR]
.RS 4
specify the minimal length of a contig (default: 100)
.RE
.PP
\fB\-errors\fR [\fIyes|no\fR]
.RS 4
search graph features which may originate from sequencing errors and remove them (default: no)
.RE
.PP
\fB\-bubble\fR [\fIvalue\fR]
.RS 4
number of rounds of p\-bubble removal to perform (default: 3)
.RE
.PP
\fB\-deadend\fR [\fIvalue\fR]
.RS 4
number of rounds of dead end removal to perform a dead end (default: 10)
.RE
.PP
\fB\-deadend\-depth\fR [\fIvalue\fR]
.RS 4
specify the maximal depth of a path to an end\-vertex by which the path shall be considered a dead end (default: 10)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-q\fR [\fIyes|no\fR]
.RS 4
suppress standard output messages (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 https://github\&.com/genometools/genometools/issues\&.