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

# hisat2-inspect(1)

HISAT2 index inspector, wrapper script

## NAME

hisat2-inspect - HISAT2 index inspector, wrapper script

## SYNOPSIS

**hisat2-inspect** \[*options*\]*\* \<ht2\_base\>*

## DESCRIPTION

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

- \<ht2\_base\>

  ht2 filename minus trailing .1.ht2/.2.ht2

-

  By default, prints FASTA records of the indexed nucleotide sequences to standard out.  With **-n**, just prints names.  With **-s**, just prints a summary of the index parameters and sequences.  With **-e**, preserves colors if applicable.

## OPTIONS

- **--large-index**

  force inspection of the 'large' index, even if a 'small' one is present.

- **-a**/--across \<int\>

  Number of characters across in FASTA output (default: 60)

- **-s**/--summary

  Print summary incl. ref names, lengths, index properties

- **-n**/--names

  Print reference sequence names only

- **--snp**

  Print SNPs

- **--ss**

  Print splice sites

- **--ss-all**

  Print splice sites including those not in the global index

- **--exon**

  Print exons

- **-e**/--ht2-ref

  Reconstruct reference from .ht2 (slow, preserves colors)

- **-v**/--verbose

  Verbose output (for debugging)

- **-h**/--help

  print detailed description of tool and its options

- **--usage**

  print this usage message

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}