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.