HISAT2-BUILD-S(1)

💖 hisat2-build-s — the small-index build bestie 💖

okay so. this is the manual page for hisat2-build-s (that's the HISAT2-BUILD-S(1) page, in User Commands land), and it's basically the small index binary of the HISAT2 indexer. it's giving "tiny but mighty" energy and honestly? we're obsessed. 🎀

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✨ SYNOPSIS ✨

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

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🌸 DESCRIPTION 🌸

so this whole thing is HISAT2 version 2.2.1, brought to you by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo). king behavior fr fr 👑

here's what the two main characters of this command are:

• reference_in — a comma-separated list of files with ref sequences. yes, commas. don't come at me with spaces, bestie. 😭
• hisat2_index_base — where the ht2 data goes, written to files with this dir/basename. that's the whole path-plus-name situation. 🦋

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⭐ OPTIONS ⭐

a whole menu of little switches, and every single one of them matters, so let's go one by one, no skipping, we're being thorough today 💅

• -c — reference sequences are given right there on the cmd line (as <reference_in>). living dangerously, iconic.
• -a/--noauto — turns OFF the automatic -p/--bmax/--dcv memory-fitting. you're on your own now, bestie.
• -p <int> — number of threads. go parallel, go fast, go slay. 🔥
• --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 — disables diff-cover. ⚠️ heads up: the algorithm becomes quadratic. that's the bad one. proceed with caution, no cap.
• -r/--noref — don't build the .3/.4.ht2 (packed reference) portion.
• -3/--justref — just build the .3/.4.ht2 (packed reference) portion. the opposite vibe of the one above, cute.
• -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. deterministic queen 🌈
• -q/--quiet — disables verbose output (for debugging). shhh. 🤫
• -h/--help — prints a detailed description of the tool and its options.
• --usage — prints this usage message.
• --version — prints version information and quits. the classic mic drop. 🎤

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and then there's this little build-info paragraph that lives at the end of the options, and it's honestly its own main character:

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}

lowkey important: that Sizeof list is {4, 8, 8, 8, 8, 8} — so int is 4 and everything else in the list is 8. bookmark it. 🍓

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👑 sign-off 👑

that's the whole page, bestie!! this was hisat2-build-s version 2.2.1, dated January 2026, and the manual page name is HISAT2-BUILD-S(1) — go forth and build those indexes, you absolute legend. no notes. periodt. 💜🧚✨