BOWTIE2-INSPECT-L(1)

💖 BOWTIE2-INSPECT-L 💖

okay bestie, gather round, because this is the little lowercase -l sibling of bowtie2-inspect from the User Commands section of your manual, and she's here to extract information from a bowtie2 index. no cap. she just wants to tell you what's inside your index, and she's gonna look cute doing it 🎀

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✨ NAME ✨

bowtie2-inspect-l — extracts information from a bowtie2 index 🦋

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🌸 SYNOPSIS 🌸

bowtie2-inspect [options]* <bt2_base>

like, the options come first, the base comes last, and that's the whole vibe fr fr 💅

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👑 DESCRIPTION 👑

Bowtie 2 version 2.5.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) — shoutout to the icon who built this, we stan 🫶

🍓 <bt2_base>

this is your bt2 filename minus the trailing .1.bt2l / .2.bt2l. so if your file is all myindex.1.bt2l, you just hand her myindex and she gets it. she's smart like that ✨

so what does she actually do when you run her? depends on your flags, bestie:

• by default — prints FASTA records of the indexed nucleotide sequences to standard out. that's the main character behaviour 💖
• with -n — just prints names. no extra, just vibes and names.
• with -s — just prints a summary of the index parameters and sequences. the whole rundown, the tl;dr, the recap nobody asked for but you lowkey need 👑

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💅 OPTIONS 💅

• -a, --across <int> — number of characters across in FASTA output. default: 60. so she wraps your sequences at 60 chars wide unless you tell her otherwise 🎀
• -n, --names — print reference sequence names only. just the names, nothing else, minimal, clean, iconic 🌸
• -s, --summary — print summary incl. ref names, lengths, index properties. the full information dump, and yes it really does include all three of those things 💜
• -o, --output — save output to filename. default is stdout, so if you don't say anything she's yelling it directly at your terminal like a group chat 😭
• -v, --verbose — verbose output (for debugging). she gets chatty. say more, bestie 🔥
• -h, --help — print this and message quit. like, she tells you what's up and then she dips 👋

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🫶 reminder bestie: -a takes an <int>, so don't forget the number. and yes, -o defaults to stdout — that's the vibe check ✨

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🌈 SEE ALSO 🌈

ngl there's no SEE ALSO section in this one, just the good stuff above 💖 and honestly? she ate. periodt.

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bowtie2-inspect-l 2.5.5 — February 2026 — and that's the whole page, bestie!! go inspect something, you absolute legend 👑✨🦋💅