BOWTIE-ALIGN-S(1)

👑 NAME 👑

okay so bestie, gather round, because this is bowtie-align-s — section 1 of the manual, the one and only ultrafast memory-efficient short read aligner 💖✨

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🌸 DESCRIPTION 🌸

here's how you call her:

usage: bowtie [-h] [--verbose] [--debug] [--large-index]

that's it, that's the whole vibe. she aligns short reads and she does it fast and lean. no cap. 🧚

✨ options ✨

• -h, --help — pops the help message and dips out. show this help message and exit, iconic behaviour honestly 👑
• --verbose — turns the verbosity on. that's the whole description bestie, I'm not gonna invent lore for it 💅
• --debug — debug mode. it's giving "tell me everything that's happening" 🔥
• --large-index — the big-index energy option. use it when your index is a main character 🎀

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🫶 the build tea ☕

not me reading the compiler receipts but okay, here's the whole thing, verbatim, no edits:

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}

like… she's 64-bit ✨ built on Debian-reproducible on Tue, 09 Dec 2025 23:19:38 +0000, compiled with gcc version 15.2.0, and yeah, the flag list is long enough to be its own group chat. it's all up there, every single one, I would never gatekeep 🙈

also, the sizes? {4, 8, 8, 8, 8, 8} for {int, long, long long, void*, size_t, off_t}. periodt.

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💜 friendly reminder that this page is bowtie-align-s from the User Commands section, so if you're looking for the general bowtie command, mind the difference bestie 🦋

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and that's the whole page!! 🫶 this was bowtie-align-s version 1.3.1, dated December 2025. go align something gorgeous, you absolute legend ⭐👑💅