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.\"     Title: gt-seed_extend
.\"    Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.78.1 <http://docbook.sf.net/>
.\"      Date: 07/29/2016
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.5.9
.\"  Language: English
.\"
.TH "GT\-SEED_EXTEND" "1" "07/29/2016" "GenomeTools 1\&.5\&.9" "GenomeTools Manual"
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.SH "NAME"
gt-seed_extend \- Calculate local alignments using the seed and extend algorithm\&.
.SH "SYNOPSIS"
.sp
\fBgt seed_extend\fR [option \&...] encseq_basename [encseq_basename]
.SH "DESCRIPTION"
.PP
\fB\-ii\fR [\fIstring\fR]
.RS 4
Input index for encseq encoded sequences
.RE
.PP
\fB\-qii\fR [\fIstring\fR]
.RS 4
Query input index (encseq)
.RE
.PP
\fB\-seedlength\fR [\fIvalue\fR]
.RS 4
Minimum length of a seed default: logarithm of input length to the basis alphabet size
.RE
.PP
\fB\-diagbandwidth\fR [\fIvalue\fR]
.RS 4
Logarithm of diagonal band width (for filter) (default: 6)
.RE
.PP
\fB\-mincoverage\fR [\fIvalue\fR]
.RS 4
Minimum coverage in two neighbouring diagonal bands (for filter) default: 2\&.5 x seedlength
.RE
.PP
\fB\-maxfreq\fR [\fIvalue\fR]
.RS 4
Maximum frequency of a k\-mer (for filter) (default: undefined)
.RE
.PP
\fB\-memlimit\fR [\fIstring\fR]
.RS 4
Maximum memory usage to determine the maximum frequency of a k\-mer (for filter) (default: undefined)
.RE
.PP
\fB\-extendxdrop\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using xdrop algorithm, /noptional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-xdropbelow\fR [\fIvalue\fR]
.RS 4
Specify xdrop cutoff score (0 means automatically defined depending on minidentity)
.RE
.PP
\fB\-extendgreedy\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using greedy algorithm, optional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-l\fR [\fIvalue\fR]
.RS 4
Minimum alignment length (for seed extension) (default: undefined)
.RE
.PP
\fB\-minidentity\fR [\fIvalue\fR]
.RS 4
Minimum identity of matches (for seed extension) (default: 80)
.RE
.PP
\fB\-a\fR [\fIvalue\fR]
.RS 4
show alignments/sequences (optional argument is number of columns per line) (default: 70)
.RE
.PP
\fB\-no\-reverse\fR [\fIyes|no\fR]
.RS 4
do not compute matches on reverse complemented strand (default: no)
.RE
.PP
\fB\-no\-forward\fR [\fIyes|no\fR]
.RS 4
do not compute matches on forward strand (default: no)
.RE
.PP
\fB\-parts\fR [\fIvalue\fR]
.RS 4
Divide data into specified number of parts (default: 1)
.RE
.PP
\fB\-kmerfile\fR [\fIyes|no\fR]
.RS 4
Use pre\-calculated k\-mers from file (if exist) (default: yes)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (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
.SH "REPORTING BUGS"
.sp
Report bugs to <gt\-users@genometools\&.org>\&.