Man page - gt-repfind(1)
Packages contas this manual
- gt-scriptfilter(1)
- gt-mmapandread(1)
- gt-gff3(1)
- gt-ltrdigest(1)
- gt-encseq(1)
- gt-extractfeat(1)
- gt-seed_extend(1)
- gt-dupfeat(1)
- gt-csa(1)
- gt-clean(1)
- gt-packedindex(1)
- gt-genomediff(1)
- gt-sketch_page(1)
- gt-compreads-refcompress(1)
- gt-splicesiteinfo(1)
- gt-extractseq(1)
- gt-compreads(1)
- gt-encseq-decode(1)
- gt-cds(1)
- gt-encseq-bitextract(1)
- gt-readjoiner(1)
- gt-tallymer-occratio(1)
- gt-tallymer(1)
- gt-sequniq(1)
- gt-id_to_md5(1)
- gt-readjoiner-prefilter(1)
- gt-seqtranslate(1)
- gt-tallymer-search(1)
- gt-condenseq(1)
- gt-seqmutate(1)
- gt-seqorder(1)
- gt-seq(1)
- gt-inlineseq_add(1)
- gt-repfind(1)
- gt-seqfilter(1)
- gt-sketch(1)
- gt-hop(1)
- gt-seqids(1)
- gt-fastq_sample(1)
- gt-compreads-refdecompress(1)
- gt-readjoiner-assembly(1)
- gt-readjoiner-overlap(1)
- gt-splitfasta(1)
- gt-seqtransform(1)
- gt-tallymer-mkindex(1)
- gt-wtree(1)
- gt-ltrharvest(1)
- gt-chseqids(1)
- gt-compreads-decompress(1)
- gt-orffinder(1)
- gt-encseq-sample(1)
- gt-encseq-md5(1)
- gt-merge(1)
- gt-gff3validator(1)
- gt-matchtool(1)
- gt-congruence(1)
- gt-tagerator(1)
- gt-gff3_to_gtf(1)
- gt-featureindex(1)
- gt-md5_to_id(1)
- gt-mkfeatureindex(1)
- gt-tirvish(1)
- gt-snpper(1)
- gt-prebwt(1)
- gt-stat(1)
- gt-speck(1)
- gt-convertseq(1)
- gt-compreads-compress(1)
- gt-interfeat(1)
- gt-chain2dim(1)
- gt-encseq-bench(1)
- gt-shulengthdist(1)
- gt-encseq-encode(1)
- gt-select(1)
- gt-uniq(1)
- gt-shredder(1)
- gt-fingerprint(1)
- gt-matstat(1)
- gt-encseq-info(1)
- gt-congruence-spacedseed(1)
- gt-encseq2spm(1)
- gt-simreads(1)
- gt(1)
- gt-dot(1)
- gt-ltrclustering(1)
- gt-seqstat(1)
- gt-mergefeat(1)
- gt-bed_to_gff3(1)
- gt-uniquesub(1)
- gt-gtf_to_gff3(1)
- gt-eval(1)
- gt-encseq-check(1)
- gt-loccheck(1)
- gt-inlineseq_split(1)
Package: genometools
apt-get install genometools
apt-get install genometools
Manuals in package:
Documentations in package:
Manual
| GT-REPFIND(1) | GenomeTools Manual | GT-REPFIND(1) |
NAME
gt-repfind - Compute maximal exact matches (and more).
SYNOPSIS
gt repfind [options] -ii indexname
DESCRIPTION
-l [value]
Specify minimum length of matches (default: 0)
-f [yes|no]
Compute forward matches (default: yes)
-r [yes|no]
Compute reverse matches (default: no)
-p [yes|no]
Compute matches on reverse strand (default: no)
-seedlength [value]
Specify minimum length of seed (default: 0)
-maxfreq [value]
Specify maximal frequency of maximal exact matches in
reference sequence (default: 0)
-extendxdrop [value]
Extend seed to both sides using xdrop algorithm, optional
parameter specifies sensitivity (default: 97)
-xdropbelow [value]
Specify xdrop cutoff score (argument 0 means undefined).
If undefined an optimal value is determined automatically depending on the
error rate
-extendgreedy [value]
Extend seed to both sides using greedy algorithm with
trimming of waves, optional parameter specifies sensitivity (default:
97)
-minidentity [value]
Specify minimum identity of matches as integer in the
range from 70 to 99 (for xdrop and greedy extension) (default: 80)
-ii [string]
Specify input index (default: undefined)
-outfmt
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
-evalue [value]
switch on evalue filtering of matches (optional argument
specifies evalue threshold) (default: 10.000000)
-scan [yes|no]
scan index rather than map it to main memory (default:
no)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to <kurtz@zbh.uni-hamburg.de>.
| 04/27/2024 | GenomeTools 1.6.5 |