'\" t
.\"     Title: gt-seed_extend
.\"    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\-SEED_EXTEND" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "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 with alphabet size as log\-base
.RE
.PP
\fB\-spacedseed\fR [\fIvalue\fR]
.RS 4
use spaced seed of length specified by option \-seedlength (optional argument specifies weight of spaced seed) (default: 0)
.RE
.PP
\fB\-diagbandwidth\fR [\fIvalue\fR]
.RS 4
Logarithm of diagonal band width in the range from 0 to 10 (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\-diagband\-stat\fR [\fI\&...\fR]
.RS 4
Compute statistics from diagonal band scores; parameter specifies kind of statistics, possible choices are sum (default: sum)
.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, optional 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\-maxmat\fR [\fIvalue\fR]
.RS 4
compute maximal matches of minimum length specified by option \-l (default: 1)
.RE
.PP
\fB\-l\fR [\fIvalue\fR]
.RS 4
Minimum length of aligned sequences (default: undefined)
.RE
.PP
\fB\-minidentity\fR [\fIvalue\fR]
.RS 4
Minimum identity of matches (for seed extension) (default: 80)
.RE
.PP
\fB\-evalue\fR [\fIvalue\fR]
.RS 4
switch on evalue filtering of matches (optional argument specifies evalue threshold) (default: 10\&.000000)
.RE
.PP
\fB\-outfmt\fR
.RS 4
specify what information about the matches to display alignment: show alignment (possibly followed by =<number> to specify width of alignment columns, default is ) seed_in_algn: mark the seed in alignment polinfo: add polishing information for shown alignment seed: abbreviation for seed\&.len seed\&.s seed\&.q failed_seed: show the coordinates of a seed extension, which does not satisfy the filter conditions fstperquery: output only the first found match per query tabsep: separate columns by tabulator, instead of space as default blast: output matches in blast format 7 (tabular with comment lines; instead of gap opens, indels are displayed) gfa2: output matches in gfa2 format custom: output matches in custom format, i\&.e\&. no columns are pre\-defined; all columns have to be specified by the user cigar: display cigar string representing alignment (no distinction between match and mismatch) cigarX: display cigar string representing alignment (distinction between match (=) and mismatch (X)) trace: display trace, i\&.e\&. a compact representation of an alignment (possibly followed by =<delta>) to specify the delta\-value; default value of delta is 50 dtrace: display trace as differences; like trace, but instead of an absolute value x, report the difference delta\-x\&. This leads to smaller numbers and thus a more compact representation s\&.len: display length of match on subject sequence s\&.seqnum: display sequence number of subject sequence subject id: display sequence description of subject sequence s\&.start: display start position of match on subject sequence s\&.end: display end position of match on subject sequence strand: display strand of match using symbols F (forward) and P (reverse complement) q\&.len: display length of match on query sequence q\&.seqnum: display sequence number of query sequence query id: display sequence description of query sequence q\&.start: display start position of match on query sequence q\&.end: display end position of match on query sequence alignment length: display length of alignment mismatches: display number of mismatches in alignment indels: display number of indels in alignment gap opens: display number of indels in alignment score: display score of match editdist: display unit edit distance identity: display percent identity of match seed\&.len: display length seed of the match seed\&.s: display start position of seed in subject seed\&.q: display start position of seed in query s\&.seqlen: display length of subject sequence in which match occurs q\&.seqlen: display length of query sequence in which match occurs evalue: display evalue bit score: display bit score
.RE
.PP
\fB\-ani\fR [\fIyes|no\fR]
.RS 4
output average nucleotide identity determined from the computed matches (which are not output) (default: no)
.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\-use\-apos\fR [\fIyes|no\fR]
.RS 4
Discard a seed only if both apos and bpos overlap with a previous successful alignment (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 https://github\&.com/genometools/genometools/issues\&.