---
name: "hisat2-build"
section: "1"
platform: "linux"
package: "hisat2"
version: "2.2.1-5+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hisat2-build"
---

# hisat2-build(1)

HISAT2 indexer, wrapper script

## 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)

- 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}