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gt-ltrharvest - Predict LTR retrotransposons.


gt ltrharvest [option ...] -index <indexname>


-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:

-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)

display help for basic options and exit

display help for all options and exit

display version information and exit


For detailed information, please refer to the manual of ltrharvest.


Report bugs to <gt-users@genometools.org>.

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