NAME
hisat2-inspect-s - HISAT2 index inspector, small index binary
SYNOPSIS
hisat2-inspect [options]* <ht2_base>
DESCRIPTION
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
- -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}