MINIMAP2.PY(1)

📦 version 2.27, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🌸 MINIMAP2.PY — the manual page, but make it make sense 🌸

okay bestie, welcome to minimap2.py, aka the minimap2 Python3 interface 💖 this little page lives in section 1 of the manual (User Commands, if you're keeping score) and it's about to tell you everything you need. no gatekeeping here, we're going through it together 🫶

✨ SYNOPSIS ✨

the vibe check of how you actually run this thing:

minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>

so yeah, you hand it a reference — either a <ref.fa> fasta or a <ref.mmi> index file, pick your fighter — and then a <query.fq> to go with it. options go up front, obviously 💅

🎀 OPTIONS 🎀

every single flag, no crumbs left behind, fr fr:

  • -x STR — set the preset. your choices are sr, map-pb, map-ont, asm5, asm10 or splice. pick one and let it cook 🔥
  • -n INT — the minimum number of minimizers ✨
  • -m INT — the minimum chaining score 👑
  • -k INT — k-mer length, classic 💜
  • -w INT — minimizer window length 🌸
  • -r INT — band width 🌈
  • -c — output the cs tag. that's it, that's the whole flag, no argument needed, she's low maintenance 💅

💖 AUTHOR 💖

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. giving credit where credit is due, as we always do 🫶

and that's the whole page, bestie. nothing else hiding in here. go run your alignments, you're gonna slay 😭✨

signing off with the receipts: this is minimap2.py version 2.17, dated June 2020, and it lives at MINIMAP2.PY(1) 🦋 periodt 💅

📦 where this page comes from