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.



When printing FASTA output, output a newline character every  bases (default: 60).


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 FTab-Chars Sequence-1 Sequence-2 ... Sequence-N

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.

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