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 09 July 2024 Compiler: gcc version 13.3.0 (Debian 13.3.0-1) 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}