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.
hisat2-inspect [options]* <ht2_base>
Main arguments
The basename of the index to be inspected. The basename is name of any of the index files but with the .X.ht2 suffix omitted. hisat2-inspect first looks in the current directory for the index files, then in the directory specified in the HISAT2_INDEXESenvironment variable.
Options
-a/--across
When printing FASTA output, output a newline character every
-n/--names
Print reference sequence names, one per line, and quit.
-s/--summary
Print a summary that includes information about index settings, as well as the names and lengths of the input sequences. The summary has this format:
Colorspace <0 or 1> SA-Sample 1 in
Fields are separated by tabs. Colorspace is always set to 0 for HISAT2.
--snp
Print SNPs, and quit.
--ss
Print splice sites, and quit.
--ss-all
Print splice sites including those not in the global index, and quit.
--exon
Print exons, and quit.
-v/--verbose
Print verbose output (for debugging).
--version
Print version information and quit.
-h/--help
Print usage information and quit.