GT-TALLYMER-SEARCH(1)

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

okay bestie, welcome to gt-tallymer-search — she's the one you call when you've got a whole index of k-mers sitting there (made by gt tallymer mkindex, iykyk) and you need to go find your query k-mers inside it. it's giving needle-in-a-haystack but make it genomics ✨

🦋 SYNOPSIS 🦋

gt tallymer search [options] -tyr tallymer-index -q queryfile0
[queryfile1..] [options]

🌸 DESCRIPTION 🌸

so basically you hand her an index (that's the -tyr thing) and some query files (that's the -q thing), and she goes hunting. here's every single knob, no gatekeeping:

  • -tyr [string] — this is where you point at your tallymer-index. default: undefined — meaning if you don't set it, there's literally nothing to search, so like… set it bestie 💅
  • -q — the query file names. plural. you can give her a whole lil squad of them (see the synopsis: queryfile0 then queryfile1..).
  • -strand [string] — which strand are we searching, queen? your options are:
    • f → forward strand
    • p → reverse complemented strand
    • fp → both, because why not have it all 🫶

default is f, so if you say nothing she assumes forward.

  • -output — the output flags, aka what she actually prints at you. the flags are: qseqnum, qpos, counts, sequence. pick your vibe ✨
  • -v [yes|no] — be verbose? default: no. turn it on if you want her to narrate.
  • -help — she explains herself, then dips. display help and exit.
  • -version — she tells you what version she is, then dips. display version information and exit.
lowkey important: -tyr has no default, so it's on you to supply the index. no index, no search, no slay. 😭

🎀 REPORTING BUGS 🎀

found something cursed? tell the devs, they wanna know fr fr:

Report bugs to <kurtz@zbh.uni-hamburg.de>.

and that's the whole page, bestie. this was GenomeTools 1.6.6, dated 11/09/2025 — go forth and tally those mers 💜🌈✨

📦 where this page comes from