HISAT2-BUILD(1)

🌸 hisat2-build — the manual page, but make it make sense 💅

okay bestie, so this is the man page for hisat2-build (yes, the HISAT2-BUILD(1) one, we're folding that in here), and it's literally the HISAT2 indexer, wrapper script. she builds indexes. she's the whole pregame before the alignment party. let's get into it 🫶

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✨ NAME ✨

hisat2-build — HISAT2 indexer, wrapper script 🔥

🎀 SYNOPSIS 🎀

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

🦋 DESCRIPTION 🦋

HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo) — iconic, we stan the author fr fr.

• reference_in — a comma-separated list of files with ref sequences. yes, comma-separated, so you can hand her a whole little squad of files and she'll take them all 💖
• hisat2_index_base — she writes the ht2 data out to files with this dir/basename. so like, whatever you name here is the name of your index babies ✨

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👑 OPTIONS 👑

one bullet per option, no skips, no skimming, we keep every single one because that's the whole vibe check:

• -c — reference sequences given on cmd line (as <reference_in>)
• --large-index — force generated index to be 'large', even if ref has fewer than 4 billion nucleotides. she said she's big and you can't tell her otherwise 💅
• -a, --noauto — disable automatic -p/--bmax/--dcv memory-fitting. no auto-tuning, you're driving manual 🏎️
• -p <int> — number of threads
• --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. that's the "this will take forever" warning. do not do this unless you mean it 😭
• -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

🧚 the build receipts (you know, the little techy flex at the bottom) 🧚

she wants you to know her stats, and honestly? fair:

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}

64-bit, Debian-built, gcc 15.2.0 energy. periodt. ⭐

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and that's the whole page bestie, no notes, she ate 💖 this was hisat2-build version 2.2.1, dated January 2026, from the HISAT2-BUILD(1) manual. go build something iconic with her 🌈 💜