hisat2

HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).

The HISAT2 MultiQC module parses summary statistics generated by versions >= v2.1.0 where the command line option --new-summary has been specified.

Note that running HISAT2 without this option (and older versions) gives log output identical to Bowtie2. These logs are indistinguishable and summary statistics will appear in MultiQC reports labelled as Bowtie2. See GitHub issues on the HISAT2 repository and the MultiQC repository for more information.

HISAT2 does not report the input file names in the log, so MultiQC takes the filename as the sample. Note that if you specify --summary-file when running HISAT2 the same summary output appears both there and in the stdout. So if you save both with different names you may end up with duplicate samples in your MultiQC report.