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HISAT2-INSPECT-S(1) User Commands HISAT2-INSPECT-S(1)

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 (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

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

32-bit Built on Debian 22 January 2023 Compiler: gcc version 12.2.0 (Debian 12.2.0-14) 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, 4, 8, 4, 4, 8}

January 2023 hisat2-inspect-s version 2.2.1