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hisat2-inspect - HISAT2 index inspector, wrapper script


hisat2-inspect [options]* <ht2_base>


HISAT2 version 2.2.1 by Daehwan Kim (,

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.


force inspection of the 'large' index, even if a 'small' one is present.
Number of characters across in FASTA output (default: 60)
Print summary incl. ref names, lengths, index properties
Print reference sequence names only
Print SNPs
Print splice sites
Print splice sites including those not in the global index
Print exons
Reconstruct reference from .ht2 (slow, preserves colors)
Verbose output (for debugging)
print detailed description of tool and its options
print this usage message

64-bit Built on Debian 05 August 2021 Compiler: gcc version 10.2.1 20210110 (Debian 10.2.1-6) 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}

August 2021 hisat2-inspect version 2.2.1