GT-REPFIND(1)

💖 NAME 💖

gt-repfind — bestie, it computes maximal exact matches (and more). that's the whole vibe. no cap. 🧬✨

🌸 SYNOPSIS 🌸

gt repfind [options] -ii indexname

🎀 DESCRIPTION 🎀

okay so listen. this is the repfind tool, and it is lowkey iconic for finding matches. it takes a whole pile of options and honestly? every single one of them is your bestie if you use them right. let's get into it 💅

🦋 OPTIONS 🦋

• -l [value] — set the minimum length of matches (default: 0). short matches? not invited.
• -f [yes|no] — compute forward matches (default: yes)
• -r [yes|no] — compute reverse matches (default: no)
• -p [yes|no] — compute matches on reverse strand (default: no)
• -seedlength [value] — set the minimum length of seed (default: 0)
• -maxfreq [value] — set the maximal frequency of maximal exact matches in reference sequence (default: 0)
• -extendxdrop [value] — extend the seed to both sides using the xdrop algorithm, and the optional parameter sets the sensitivity (default: 97)
• -xdropbelow [value] — set the xdrop cutoff score (argument 0 means undefined). if it's undefined, an optimal value is determined automatically depending on the error rate ✨
• -extendgreedy [value] — extend the seed to both sides using the greedy algorithm with trimming of waves, and the optional parameter sets the sensitivity (default: 97)
• -minidentity [value] — set the minimum identity of matches as an integer in the range from 70 to 99 (this is for xdrop and greedy extension) (default: 80)
• -ii [string] — specify the input index (default: undefined) — this one is kinda the whole point, don't skip it 🫶
• -outfmt — specify what information about the matches to display. and girl, there are SO many choices:
  • alignment: show alignment (possibly followed by =<number> to specify width of alignment columns, default is )
  • seed_in_algn: mark the seed in alignment
  • polinfo: add polishing information for shown alignment
  • seed: abbreviation for seed.len seed.s seed.q
  • failed_seed: show the coordinates of a seed extension, which does not satisfy the filter conditions
  • fstperquery: output only the first found match per query
  • tabsep: separate columns by tabulator, instead of space as default
  • blast: output matches in blast format 7 (tabular with comment lines; instead of gap opens, indels are displayed)
  • gfa2: output matches in gfa2 format
  • custom: output matches in custom format, i.e. no columns are pre-defined; all columns have to be specified by the user
  • cigar: display cigar string representing alignment (no distinction between match and mismatch)
  • cigarX: display cigar string representing alignment (distinction between match (=) and mismatch (X))
  • trace: display trace, i.e. a compact representation of an alignment (possibly followed by =<delta>) to specify the delta-value; default value of delta is 50
  • dtrace: display trace as differences; like trace, but instead of an absolute value x, report the difference delta-x. This leads to smaller numbers and thus a more compact representation
  • s.len: display length of match on subject sequence
  • s.seqnum: display sequence number of subject sequence
  • subject id: display sequence description of subject sequence
  • s.start: display start position of match on subject sequence
  • s.end: display end position of match on subject sequence
  • strand: display strand of match using symbols F (forward) and P (reverse complement)
  • q.len: display length of match on query sequence
  • q.seqnum: display sequence number of query sequence
  • query id: display sequence description of query sequence
  • q.start: display start position of match on query sequence
  • q.end: display end position of match on query sequence
  • alignment length: display length of alignment
  • mismatches: display number of mismatches in alignment
  • indels: display number of indels in alignment
  • gap opens: display number of indels in alignment
  • score: display score of match
  • editdist: display unit edit distance
  • identity: display percent identity of match
  • seed.len: display length seed of the match
  • seed.s: display start position of seed in subject
  • seed.q: display start position of seed in query
  • s.seqlen: display length of subject sequence in which match occurs
  • q.seqlen: display length of query sequence in which match occurs
  • evalue: display evalue
  • bit score: display bit score
• -evalue [value] — switch on evalue filtering of matches, and the optional argument specifies the evalue threshold (default: 10.000000)
• -scan [yes|no] — scan the index rather than map it to main memory (default: no)
• -v [yes|no] — be verbose (default: no) — she talks a lot and honestly we love that for her 🗣️
• -help — display help and exit
• -version — display version information and exit

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🐛 REPORTING BUGS 🐛

found a bug? don't be shy, tell on it. report bugs to <kurtz@zbh.uni-hamburg.de> 💌

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okay that's the whole page, bestie!! you ate this 🫶 this was GenomeTools 1.6.6, dated 11/09/2025 — go forth and find those matches, main character 🌈💖