BOWTIE2-BUILD-S(1)

💫 BOWTIE2-BUILD-S 💫

okay bestie, so this is a page from the User Commands manual — it's bowtie2-build-s(1), the little sibling that builds you a colorspace index for Bowtie 2. iykyk. it's giving "i make the index, you go do the aligning" and honestly? iconic. let's get into it 🎀

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✨ NAME ✨

bowtie2-build-s — building a colorspace index for bowtie2

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🦋 SYNOPSIS 🦋

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

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🌸 DESCRIPTION 🌸

so first things first, the vibes check: Bowtie 2 version 2.5.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea). yes, the actual person. king behavior 👑

now the two things you gotta hand over:

• reference_in — a comma-separated list of files with ref sequences. basically "here's the DNA, bestie" 🧬
• bt2_index_base — write bt2 data to files with this dir/basename. so like, this is the name you want your index files to have, and the dir part decides where they land.

💀 *** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. *** — no cap, that's the compatibility line, don't lose it.

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💅 OPTIONS 💅

here's the full menu, bestie — every single one, no skipping, i would never gatekeep 🫶

• -f — reference files are Fasta (default). this is the default behavior, so if you say nothing, you get Fasta. slay.
• -c — reference sequences given on cmd line (as <reference_in>). like, straight from the command line, no file needed.
• -a/--noauto — disable automatic -p/--bmax/--dcv memory-fitting. you're turning off the auto-pilot on memory stuff.
• -p/--packed — use packed strings internally; slower, less memory. so yeah, it trades speed for RAM. pick your fighter 🌈
• --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 (algorithm becomes quadratic). ⚠️ quadratic!!! that's the "it's gonna get slow" warning, okay? noted fr fr.
• -r/--noref — don't build .3/.4 index files.
• -3/--justref — just build .3/.4 index files. only those. nothing else. minimal queen 💜
• -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, that is exactly what it says. i am not editorializing. we report, we do not fix 🙈)
• --h/--help — print this message and quit.
• --version — print version information and quit.

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⭐ that's the whole thing ⭐

go build that index, bestie, you're literally the main character of this pipeline 👑

much love from bowtie2-build-s 2.5.5, brought to you in February 2026 — catch you in the next man page 💖✨🎀