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.