hisat2-inspect

Reference

hisat2-inspect extracts information from a HISAT2 index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A/C/G/T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n/--names option or a more verbose summary using the -s/--summary option.

Category

Mapping

Usage

hisat2-inspect [options]* <ht2_base>

Manual

Required arguments

  • <ht2_base>: HT2 filename minus trailing .1.ht2/.2.ht2.

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 including reference names, lengths, and index properties.
  • -n / --names: Print reference sequence names only.
  • --snp: Print SNPs.
  • --ss: Print splice sites.
  • --ss-all: Print all 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 a detailed description of the tool and its options.
  • --usage: Print this usage message.

Note: By default, the tool prints FASTA records of the indexed nucleotide sequences to standard output.

Share your experience or ask a question