HISAT2-BUILD-L(1)

🌸 HISAT2-BUILD-L(1) — bestie, it's the HISAT2 indexer, large index binary 💅

okay so you went looking for the hisat2-build-l manual page and you found me instead, which, honestly, slay. this is the big-sister version of the HISAT2 index builder — the one that makes the large index .ht2l files. let's get into it 🦋

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✨ NAME ✨

hisat2-build-l — HISAT2 indexer, large index binary. that's the whole vibe. it builds indexes. it's large. it's iconic. 👑

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✨ SYNOPSIS ✨

hisat2-build [options]* <reference_in> <ht2_index_base>

like yeah, the binary is called hisat2-build-l but it literally introduces itself as hisat2-build in the usage line. main character energy, no notes. 💖

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✨ DESCRIPTION ✨

HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo) — king behavior fr fr 🙌

reference_in a comma-separated list of files with ref sequences. that's it, that's the list. feed it your reference, bestie 🧚

hisat2_index_base write ht2l data to files with this dir/basename. so basically wherever you point it, that's where the index lives. choose wisely because it's not shy about writing files 🎀

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✨ OPTIONS ✨

one billion options? no. but like, a lot? yes. here's every single one, no skipping, no cap:

• -c — reference sequences given on cmd line (as <reference_in>)
• -a, --noauto — disable automatic -p/--bmax/--dcv memory-fitting
• -p <int> — number of threads. more threads = more zoomies 🏃💨
• --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 (algorithm becomes quadratic)

⚠️ bestie. quadratic. i'm just saying what the manpage says. don't do it unless you truly know what you're doing 😭

• -r, --noref — don't build .3/.4.ht2 (packed reference) portion
• -3, --justref — just build .3/.4.ht2 (packed reference) portion
• -o, --offrate <int> — SA is sampled every 2^offRate BWT chars (default: 5)
• -t, --ftabchars <int> — # of chars consumed in initial lookup (default: 10)
• --localoffrate <int> — SA (local) is sampled every 2^offRate BWT chars (default: 3)
• --localftabchars <int> — # of chars consumed in initial lookup in a local index (default: 6)
• --snp <path> — SNP file name
• --haplotype <path> — haplotype file name
• --ss <path> — Splice site file name
• --exon <path> — Exon file name
• --repeat-ref <path> — Repeat reference file name
• --repeat-info <path> — Repeat information file name
• --repeat-snp <path> — Repeat snp file name
• --repeat-haplotype <path> — Repeat haplotype file name
• --seed <int> — seed for random number generator 🎲
• -q, --quiet — disable 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 (yes this is part of the page)

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}

like it really said "here's my whole compiler lore" and i respect it 💜

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🌈 SEE ALSO 🌈

nothing here bestie, the original page doesn't list any references. you're on your own but you're doing great 🫶

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🫶 cute sign-off

hisat2-build-l version 2.2.1, dated January 2026. that's the tea, that's the source, that's the date. go forth and build your large index, you absolute legend. periodt 💅✨🌸