Man page - gt-ltrharvest(1)
Packages contas this manual
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- 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)
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- gt-seqids(1)
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- 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)
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- gt-encseq-md5(1)
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- 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
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Manual
| GT-LTRHARVEST(1) | GenomeTools Manual | GT-LTRHARVEST(1) |
NAME
gt-ltrharvest - Predict LTR retrotransposons.
SYNOPSIS
gt ltrharvest [option ...] -index <indexname>
DESCRIPTION
-index [string]
specify the name of the enhanced suffix array index
(mandatory) (default: undefined)
-range [start end]
specify range in the input sequence(s) in which LTR pairs
are searched (default: [0..0])
-seed [value]
specify minimum seed length for exact repeats (default:
30)
-minlenltr [value]
specify minimum length for each LTR (default: 100)
-maxlenltr [value]
specify maximum length for each LTR (default: 1000)
-mindistltr [value]
specify minimum distance of LTR startpositions (default:
1000)
-maxdistltr [value]
specify maximum distance of LTR startpositions (default:
15000)
-similar [value]
specify similaritythreshold in range [1..100%] (default:
85.000000)
-mintsd [value]
specify minimum length for each TSD (default: 4)
-maxtsd [value]
specify maximum length for each TSD (default: 20)
-motif [string]
specify 2 nucleotides startmotif + 2 nucleotides
endmotif: ** (default: undefined)
-motifmis [value]
specify maximum number of mismatches in motif [0,3]
(default: 4)
-vic [value]
specify the number of nucleotides (to the left and to the
right) that will be searched for TSDs and/or motifs around 5' and 3' boundary
of predicted LTR retrotransposons (default: 60)
-overlaps [...]
specify no|best|all (default: best)
-xdrop [value]
specify xdropbelowscore for extension-alignment (default:
5)
-mat [value]
specify matchscore for extension-alignment (default:
2)
-mis [value]
specify mismatchscore for extension-alignment (default:
-2)
-ins [value]
specify insertionscore for extension-alignment (default:
-3)
-del [value]
specify deletionscore for extension-alignment (default:
-3)
-v [yes|no]
verbose mode (default: no)
-tabout [yes|no]
show old tabular output instead of GFF3 on stdout
(default: yes)
-seqids [yes|no]
use sequence descriptions instead of sequence numbers in
GFF3 output (default: no)
-md5 [yes|no]
add MD5 hashes to seqids in GFF3 output (default:
no)
-longoutput [yes|no]
additional motif/TSD output (default: no)
-out [string]
specify FASTA outputfilename (default: undefined)
-outinner [string]
specify FASTA outputfilename for inner regions (default:
undefined)
-gff3 [string]
specify GFF3 outputfilename (default: undefined)
-offset [value]
offset added to GFF3 coordinates (default: 0)
-scan [yes|no]
scan the index sequentially instead of mapping it into
memory entirely (default: yes)
-help
display help for basic options and exit
-help+
display help for all options and exit
-version
display version information and exit
ADDITIONAL INFORMATION
For detailed information, please refer to the manual of ltrharvest.
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.
| 04/27/2024 | GenomeTools 1.6.5 |