HISAT2-INSPECT-L(1)

💖 NAME 💖

hisat2-inspect-l — the HISAT2 index inspector, but make it the large index binary. Bestie, this is the one that peeks inside your huge .ht2l index and tells you everything it knows 🕵️♀️✨

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🌸 SYNOPSIS 🌸

hisat2-inspect [options]* <ht2_base>

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🦋 DESCRIPTION 🦋

HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo). Yeah, the whole thing was built by one iconic human, we love to see it 👑

<ht2_base>

That's your ht2 filename, minus the trailing .1.ht2l/.2.ht2l. So like, strip the suffix off and hand over the base name, okay? 💅

So what does it actually do out of the box? By default it prints FASTA records of the indexed nucleotide sequences to standard out. That's the no-flags vibe ✨

But wait, there's more, and each flag swaps the whole energy:

• With -n, it just prints names. Names only. No sequences, no small talk.
• 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 ✨

• -a/--across <int> — Number of characters across in FASTA output (default: 60). Yes bestie, you can control the line width, go wild 🎀
• -s/--summary — Print summary incl. ref names, lengths, index properties.
• -n/--names — Print reference sequence names only. Sometimes you just want the names, and honestly? Valid.
• --snp — Print SNPs.
• --ss — Print splice sites.
• --ss-all — Print splice sites including those not in the global index. The extended cut 👑
• --exon — Print exons.
• -e/--ht2-ref — Reconstruct reference from .ht2l (slow, preserves colors). Okay so heads up: it says slow and it means slow 😭 but the colors stay, so.
• -v/--verbose — Verbose output (for debugging).
• -h/--help — print detailed description of tool and its options.
• --usage — print this usage message.

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🌟 THE BUILD RECEIPTS 🌟

Here's the exact build info, verbatim, because numbers are sacred and I do not round 💯

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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And that's the whole page, bestie 🫶 This was hisat2-inspect-l version 2.2.1, dated January 2026 — the large-index inspector, still serving looks. Go inspect something iconic 💖✨