GT-SEED_EXTEND(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 GT-SEED_EXTEND 💖

okay bestie, gather round, because we're about to talk about gt-seed_extend — the GenomeTools girlie whose whole entire job is calculating local alignments with the seed and extend algorithm. it's giving find the cute matching bits, then grow them. no cap. 🧬✨

✨ SYNOPSIS ✨

gt seed_extend [option ...] encseq_basename [encseq_basename]

yep. that's the whole vibe. one basename, or lowkey two if you're feeling generous. 💅

🌸 DESCRIPTION 🌸

okay so here's the tea, option by option, and I am not skipping a single one because every flag is a main character here:

  • -ii [string] — the input index for encseq encoded sequences. that's the source material, babe. 📖
  • -qii [string] — the query input index (encseq). yes, a separate index, for the queries. she's got range. 💜
  • -seedlength [value] — minimum length of a seed. default? it's the logarithm of input length, with alphabet size as the log-base. math girlies rise. 🧮
  • -spacedseed [value] — use a spaced seed of length specified by option -seedlength. the optional argument specifies the weight of the spaced seed. (default: 0)
  • -diagbandwidth [value] — logarithm of diagonal band width, in the range from 0 to 10, for the filter. (default: 6) 🎚️
  • -mincoverage [value] — minimum coverage in two neighbouring diagonal bands, for the filter. default: 2.5 x seedlength. yes, it literally scales with seedlength. iconic. 📈
  • -diagband-stat [...] — compute statistics from diagonal band scores. the parameter specifies the kind of statistics; possible choices are sum. (default: sum) 📊
  • -maxfreq [value] — maximum frequency of a k-mer, for the filter. (default: undefined) 🚫
  • -memlimit [string] — maximum memory usage, used to determine the maximum frequency of a k-mer, for the filter. (default: undefined) 🧠
  • -extendxdrop [value] — extend the seed to both sides using the xdrop algorithm. the optional parameter specifies sensitivity. (default: 97) 🌱
  • -xdropbelow [value] — specify the xdrop cutoff score. (0 means it's automatically defined depending on minidentity.) ✂️
  • -extendgreedy [value] — extend the seed to both sides using the greedy algorithm. the optional parameter specifies sensitivity. (default: 97) 🤑
  • -maxmat [value] — compute maximal matches of minimum length specified by option -l. (default: 1)
  • -l [value] — minimum length of aligned sequences. (default: undefined) 📏
  • -minidentity [value] — minimum identity of matches, for seed extension. (default: 80) 🪞
  • -evalue [value] — switch on evalue filtering of matches. the optional argument specifies the evalue threshold. (default: 10.000000) 🎯
  • -outfmt — specify what information about the matches to display. okay this one is a whole mood board, so here are ALL the choices, fr fr:
    • 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
  • -ani [yes|no] — output average nucleotide identity determined from the computed matches (which are not output). (default: no) 🧪
  • -no-reverse [yes|no] — do not compute matches on the reverse complemented strand. (default: no) ↩️
  • -no-forward [yes|no] — do not compute matches on the forward strand. (default: no) ↪️
  • -use-apos [yes|no] — Discard a seed only if both apos and bpos overlap with a previous successful alignment. (default: no) 🫶
  • -parts [value] — Divide data into specified number of parts. (default: 1) 🍰
  • -kmerfile [yes|no] — Use pre-calculated k-mers from file (if exist). (default: yes) 📂
  • -v [yes|no] — be verbose. (default: no) 🗣️
  • -help — display help and exit. 🆘
  • -version — display version information and exit. 🏷️

💌 REPORTING BUGS 💌

found a bug? don't be shy, bestie, report it at https://github.com/genometools/genometools/issues. the maintainers wanna hear it. 🐛✨

okay that's the whole page, and honestly? she ate. 💅

GenomeTools 1.6.6 — dated 11/09/2025. mwah. 🎀🦋💖
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