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 (Ubuntu 13.3.0-2ubuntu1) Options: -O3
       -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=3  -std=c++11  Sizeof  {int,  long,  long  long,  void*,
       size_t, off_t}: {4, 8, 8, 8, 8, 8}

hisat2-inspect version 2.2.1                        July 2024                                  HISAT2-INSPECT(1)