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>
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.
When printing FASTA output, output a newline character every
Print reference sequence names, one per line, and quit.
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.
Print SNPs, and quit.
Print splice sites, and quit.
Print splice sites including those not in the global index, and quit.
Print exons, and quit.
Print verbose output (for debugging).
Print version information and quit.
Print usage information and quit.