hisat2-inspect(1)

Usage

hisat2-inspect [options] * <ht2_base>

Overview

HISAT2 version 2.2.1 by Daehwan Kim ([email protected], 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}

Releases

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

9
10
11
12
13

--usage since Debian 11 (Bullseye).

--help until Debian 10 (Buster).