BOWTIE-BUILD(1)

💖 NAME 💖

okay bestie, gather round — bowtie-build is the girl who builds a colorspace index for bowtie. that's her whole job. she eats a reference and spits out an index. iconic behavior tbh 🎀

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✨ SYNOPSIS ✨

bowtie-build [options]* <reference_in> <ebwt_outfile_base>

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🦋 DESCRIPTION 🦋

two lil arguments, both absolutely carrying:

• reference_in — a comma-separated list of files with ref sequences. yes, comma. like you're texting a whole group chat of genomes 💅
• ebwt_outfile_base — write Ebwt data to files with this dir/basename. that's the vibe. that's the location. that's the name prefix. slay.

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🎀 OPTIONS 🎀

• -f — reference files are Fasta (this is the default, so if you say nothing, this is what you get 🫶)
• -c — reference sequences given on cmd line instead (as <seq_in>)
• --large-index — force the generated index to be 'large', even if ref has fewer than 4 billion nucleotides. she said big index energy whether you need it or not 👑
• -a/--noauto — disable automatic -p/--bmax/--dcv memory-fitting. you're driving manual, no cap
• -p/--packed — use packed strings internally; slower, uses less mem. the tradeoff queen 🌸
• --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. heads up bestie: the algorithm becomes quadratic 😭 not me warning you fr fr
• -r/--noref — don't build .3/.4.ebwt (packed reference) portion
• -3/--justref — just build .3/.4.ebwt (packed reference) portion. the opposite twin, obsessed 💜
• -o/--offrate <int> — SA is sampled every 2^offRate BWT chars (default: 5)
• -t/--ftabchars <int> — # of chars consumed in initial lookup (default: 10)
• --threads <int> — # of threads. give her more cores, she'll move faster ✨
• --ntoa — convert Ns in reference to As
• --seed <int> — seed for random number generator
• -q/--quiet — verbose output (for debugging)
• -h/--help — print detailed description of tool and its options
• --usage — print this usage message
• --version — print version information and quit

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🔧 the build receipts (keepin it exact)

• 64-bit Built on Debian-reproducible Tue, 09 Dec 2025 23:19:38 +0000
• Compiler: gcc version 15.2.0 Options: -O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -Werror=implicit-function-declaration -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=.=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=.=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=.=/usr/src/bowtie-1.3.1-3build1 -std=c++03 -Wl,-Bsymbolic-functions -Wl,--package-metadata={%22type%22:%22deb%22%2C%22os%22:%22ubuntu%22%2C%22name%22:%22bowtie%22%2C%22version%22:%221.3.1-3build1%22%2C%22architecture%22:%22amd64%22} -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now

Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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no cap: if you're trying to remember ONE thing, it's that bowtie-build [options]* <reference_in> <ebwt_outfile_base> is the shape of her whole life 💀

go build that index bestie, you ate, periodt 💅🌈🦋

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that's the whole page, and just so we're clear: this is bowtie-build version 1.3.1, dated December 2025 — and yes, we're sitting in the BOWTIE-BUILD(1) user-commands section the whole time. bye bestie, ily, go index something 🫶💖