HISAT2
Maps DNA or RNA reads against a genome or a population of genomes
The 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.
File search patterns
hisat2:
contents: "HISAT2 summary stats:"