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  14  October  2022  Compiler:   gcc   version   12.2.0   (Ubuntu
       12.2.0-9ubuntu1)   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}