GT-LTRHARVEST(1)

💖 GT-LTRHARVEST 💖

okay bestie so this is gt-ltrharvest from the GenomeTools Manual (yes it's section 1, we love a classic) — and she's here to Predict LTR retrotransposons 🧬✨ like that's literally her whole job and she eats every time.

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✨ SYNOPSIS ✨

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

that's it, that's the whole vibe. give her an index and she'll go off 👑

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🌸 DESCRIPTION 🌸

so like, every single flag, right here, in order, no skips, no cuts, we're doing the full album not just the singles 💅

• -index [string] — specify the name of the enhanced suffix array index. mandatory, like you literally cannot skip this one bestie, she will not run without it. (default: undefined)
• -range [start end] — specify the 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 (the deluxe edition fr fr)
• -version — display version information and exit 🏷️

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📚 ADDITIONAL INFORMATION 📚

For detailed information, please refer to the manual of ltrharvest. (she's got the lore, this one's just the group chat summary)

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🐛 REPORTING BUGS 🐛

Report bugs to https://github.com/genometools/genometools/issues.

not me begging you to actually file the issue instead of just complaining in the group chat 🙈 they can't fix what they can't see, bestie

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and that's the whole page!! this cutie is GenomeTools 1.6.6, dated 11/09/2025, and honestly? she's iconic, she's giving main character energy, go predict some retrotransposons 💖✨🎀🦋🌸💅🫶👑🌈⭐💜🍓🧚