Man page - gt-ltrharvest(1)
Packages contains this manual
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- gt-congruence-spacedseed(1)
- gt-id_to_md5(1)
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apt-get install genometools
Manual
GT-LTRHARVEST
NAMESYNOPSIS
DESCRIPTION
ADDITIONAL INFORMATION
REPORTING BUGS
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.