BOWTIE2-BUILD(1)

📦
version 2.5.5 · 9 versions
, in ubuntu stonking

✨ NAME ✨

bowtie2-build — okay so it's a wrapper for bowtie2-build-*, that's the whole vibe 💅

🌸 SYNOPSIS 🌸

bowtie2-build [options]* <reference_in> <bt2_index_base>

🦋 DESCRIPTION 🦋

So this is Bowtie 2 version 2.5.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) — yeah, the whole manual page is literally this, bestie, and it's iconic 💖

Here's the tea on the two arguments:

  • reference_in — a comma-separated list of files with ref sequences. That's it, that's the job 🎀
  • bt2_index_base — it writes bt2 data to files with this dir/basename. So like, wherever you point it, that's where the index lands ✨
* Bowtie 2 indexes will work with Bowtie v1.2.3 and later. * — no cap, that's a promise from the manpage itself 🫶

👑 OPTIONS 👑

Okay bestie, here's the full roster, no skips, no summaries, every single one 💅

  • -f — reference files are Fasta. (This is the default, so if you do nothing, congrats, you already picked it 💖)
  • -c — reference sequences are given on the cmd line instead (as <reference_in>) ⭐
  • --large-index — force the generated index to be 'large', even if the ref has fewer than 4 billion nucleotides. Big index energy, even when it's not 👑
  • --debug — use the debug binary; slower, assertions enabled 🐛
  • --verbose — log the issued command 📝
  • -a/--noauto — disable automatic -p/--bmax/--dcv memory-fitting 🙈
  • -p/--packed — use packed strings internally; slower, less memory 🌸
  • --bmax <int> — max bucket sz for blockwise suffix-array builder 🍓
  • --bmaxdivn <int> — max bucket sz as divisor of ref len (default: 4) 🔢
  • --dcv <int> — diff-cover period for blockwise (default: 1024) 🌈
  • --nodc — disable diff-cover, and heads up: the algorithm becomes quadratic 😭 careful bestie
  • -r/--noref — don't build .3/.4 index files 💀
  • -3/--justref — just build .3/.4 index files ✨
  • -o/--offrate <int> — SA is sampled every 2^<int> BWT chars (default: 5) 🎀
  • -t/--ftabchars <int> — # of chars consumed in initial lookup (default: 10) 🔥
  • --threads <int> — # of threads 🧚
  • --seed <int> — seed for random number generator 🎲
  • -q/--quiet — verbose output (for debugging). Yes bestie, that's literally what the page says, I'm just the messenger 💜
  • --h/--help — print this message and quit 🫶
  • --version — print version information and quit ⭐

bowtie2-build 2.5.5, February 2026 — that's the source and the date, mwah, take care of her 💖💅✨

📦 where this page comes from