gt-ltrharvest1
Predict ltr retrotransposons.
Usage
gt ltrharvest
[option ...]
-index
<indexname>
Overview
-
-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.
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.