hisat2-build1

Hisat2 indexer, wrapper script

Usage

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

Overview

HISAT2 version 2.2.1 by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)

`reference_in`	comma-separated list of files with ref sequences
`hisat2_index_base`	write ht2 data to files with this dir/basename

Options

-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

-a/--noauto: disable automatic -p/--bmax/--dcv memory-fitting

-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)

`-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

64-bit Built on Debian 28 March 2025 Compiler: gcc version 14.2.0 (Debian 14.2.0-19) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Releases

5 releases since Debian 9 (Stretch); the text changed 4 times.

--repeat-haplotype since Debian 11 (Bullseye); --repeat-info since Debian 11 (Bullseye); --repeat-ref since Debian 11 (Bullseye); --repeat-snp since Debian 11 (Bullseye).