HISAT2-INSPECT(1)

💖 HISAT2-INSPECT(1) — the hisat2-inspect manual, bestie edition 💖

okay so you've found your way to hisat2-inspect, the wrapper script that's basically the HISAT2 index inspector. manual name? <pink>HISAT2-INSPECT</pink>, section 1, and it lives in User Commands. she's giving very much "let me peek inside your index and tell you everything about it" energy and honestly? iconic. 🎀

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✨ NAME ✨

hisat2-inspect — HISAT2 index inspector, wrapper script 🌸

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🦋 SYNOPSIS 🦋

hisat2-inspect [options]* <ht2_base>

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💅 DESCRIPTION 💅

so this is HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo). hi Daehwan, you ate. 👑

<ht2_base> 💜

that's your ht2 filename minus the trailing .1.ht2/.2.ht2. yes girl, you just leave the extension at home. 🫶

by default, it prints FASTA records of the indexed nucleotide sequences to standard out. no cap, that's just what happens if you don't say otherwise.

then you got your little modes, and they're all a vibe:

• with -n, it just prints names 💫
• with -s, it just prints a summary of the index parameters and sequences 📋
• with -e, it preserves colors if applicable 🌈

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🌟 OPTIONS 🌟

• --large-index — forces inspection of the 'large' index, even if a 'small' one is present. she said we're going big or going home. 🔥
• -a/--across <int> — number of characters across in FASTA output. default? <int> is <pink>60</pink>. 📏
• -s/--summary — print summary incl. ref names, lengths, index properties. the whole tea, basically. 🍵
• -n/--names — print reference sequence names only. short, sweet, to the point. ✨
• --snp — print SNPs. 🧬
• --ss — print splice sites. ✂️
• --ss-all — print splice sites including those not in the global index. she's thorough like that. 🌸
• --exon — print exons. 💖
• -e/--ht2-ref — reconstruct reference from .ht2. heads up bestie: slow, but it preserves colors. 😭🖌️
• -v/--verbose — verbose output, for debugging. loud and proud, we respect it. 🗣️
• -h/--help — print detailed description of tool and its options. your bestie when you're lost. 🫶
• --usage — print this usage message. the lil reminder text. 💌

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also, for the build girlies: 64-bit Built on Debian 21 January 2026 Compiler: gcc version 15.2.0 (Ubuntu 15.2.0-11ubuntu1) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=3 -std=c++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

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🌈 SEE ALSO 🌈

okay technically there's no SEE ALSO section in this one, so consider this your SEE ALSO: go read <ht2_base> again, go run --help, and slay. 💅

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byeee 💖 this was hisat2-inspect version 2.2.1, dated January 2026, and yes the manual really is named <hotpink>HISAT2-INSPECT(1)</hotpink>. mwah, go inspect something. 💋✨