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.