GT-TALLYMER-MKINDE(1)

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

💖 gt-tallymer-mkindex — the GenomeTools glow-up 💖

okay bestie, pull up a chair, because this is the gt-tallymer-mkindex manual page (section 1, the classic command-line-girlies section) from the GenomeTools manual, and she is serving k-mer realness. ✨

🌸 NAME 🌸

gt-tallymer-mkindex — counts and indexes k-mers in the enhanced suffix array you hand her, for one fixed value of k. that's it, that's the whole job, and she does it flawlessly. no cap. 👑

🦋 SYNOPSIS 🦋

gt tallymer mkindex [options] -esa suffixerator-index [options]

💅 DESCRIPTION 💅

so the way this works is you've already got yourself an enhanced suffix array (built by suffixerator, duh), and now you want the k-mers counted and indexed out of it. here's every single knob and dial, fr fr, no skips:

  • -esa [string] — this is where you specify the suffixerator-index. and bestie, listen — it's mandatory. like, you literally cannot run this without it. (default: undefined) 🚨
  • -mersize [value] — specifies the mer size, aka your k. (default: 20)
  • -minocc [value] — the minimum occurrence number for the mers to output/index. (default: 0)
  • -maxocc [value] — the maximum occurrence number for the mers to output/index. (default: 0)
  • -pl [value] — specifies the prefix length for bucket boundary construction. the recommendation here is chef's kiss: use it without an argument, and then a reasonable prefix length is automatically determined for you. let her cook. 🍓 (default: 0)
  • -indexname [string] — stores the mers specified by the options -maxocc and -minocc in an index. (default: undefined)
  • -counts [yes|no] — stores counts of the mers. (default: no)
  • -scan [yes|no] — reads the enhanced suffix array sequentially instead of mapping it to memory. (default: no)
  • -v [yes|no] — be verbose, aka let her yap. (default: no)
  • -help — displays help and exits. 🫶
  • -version — displays version information and exits. ⭐

😭 REPORTING BUGS 😭

found a bug? do NOT suffer in silence, tell a grown-up (the maintainer). report bugs to <kurtz@zbh.uni-hamburg.de>. 💌

and that's the whole page, you ate that. 🎀 this was the GenomeTools 1.6.6 manual, dated 11/09/2025 — so if you're reading this, hi from that exact moment in time, hope the k-mers are k-mer-ing. mwah. 💜🌈

📦 where this page comes from