BOWTIE2-INSPECT(1)

📦
version 2.5.5 · 9 versions
, in ubuntu stonking

🎀 BOWTIE2-INSPECT(1) 🎀

okay bestie come CLOSE, this is the User Commands corner of the manual and we're about to peek inside a Bowtie 2 index like it's your situationship's notes app 💅

✨ NAME ✨

bowtie2-inspect — the wrapper glow-up around the bowtie2-inspect-* index, iykyk 🦋

🌸 SYNOPSIS 🌸

bowtie2-inspect [options]* <bt2_base>

💖 DESCRIPTION 💖

So first things first, the queen herself: Bowtie 2 version 2.5.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 👑

  • <bt2_base> — this is literally your bt2 filename minus the trailing .1.bt2/.2.bt2. That's it, that's the whole vibe, no cap.

Now for the default behaviour, and it's giving main character energy: by default it prints FASTA records of the indexed nucleotide sequences to standard out ⭐

  • With -n? Just prints names. short n sweet 🍓
  • With -s? Just prints a summary of the index parameters and sequences. a little report card 📋

✨ OPTIONS ✨

  • --large-index — forces inspection of the large index, even if a small one is hanging around being present. like, we're choosing violence, okay? 🔥
  • --debug — uses the debug binary; slower, assertions enabled. it's the paranoid friend who double-checks everything 😭 (slower tho, fr fr)
  • --verbose — logs the issued command. receipts on receipts 🧾
  • -a/--across <int> — number of characters across in FASTA output (default: 60). customize your line aesthetic 💅
  • -n/--names — print reference sequence names only. just the names, no baggage 🎀
  • -s/--summary — print summary incl. ref names, lengths, index properties. the whole lore drop 📖
  • -o/--output — save output to filename (default stdout). no, stdout is the default, so if you don't say anything it just spills out into your terminal 🌈
  • -v/--verbose — verbose output (for debugging). yes queen, talk to me 🫶
  • -h/--help — prints this and message quit. the classic escape hatch 🙈
lowkey a warning-ish reminder: --debug is slower because assertions are enabled. that's the whole tradeoff, don't act surprised bestie 💜

that's the whole page, you ate it 💅 bowtie2-inspect 2.5.5, dated February 2026 — mwah, see you in the next manpage 🦋✨

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