BOWTIE2-BUILD-L(1)

💖 NAME 💖

bowtie2-build-l — building a colorspace index for bowtie2 ✨

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🌸 SYNOPSIS 🌸

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

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🦋 DESCRIPTION 🦋

okay so bestie, this whole thing is Bowtie 2 version 2.5.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) 💅

Here's the tea on the two positional args you gotta hand over:

• reference_in — a comma-separated list of files with ref sequences 📚
• bt2_index_base — write bt2l data to files with this dir/basename 🎀

* Bowtie 2 indexes will work with Bowtie v1.2.3 and later. * — no cap, that's the compatibility vibe check right there 👑

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✨ OPTIONS ✨

• -f — reference files are Fasta (default) 🧬
• -c — reference sequences given on cmd line (as <reference_in>) ⌨️
• -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 (algorithm becomes quadratic) 😭
• -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) 🫶
• --h, --help — print this message and quit 💬
• --version — print version information and quit 🏷️

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and that's the whole page, bestie!! 🌈 this lil cutie is bowtie2-build-l 2.5.5, dated February 2026 ⭐ go forth and build those colorspace indexes, you absolute icon 👑💖