HISAT2

HISAT2 is a sensitive spliced alignment program for mapping RNA-sequencing data. It utilizes a combination of small FM indexes with a singular large FM index to collectively cover the whole genome and effectively align across exons. Built upon bowtie2 and hisat.

tip

Note several other tools load with this module and can be seen running the following command: report_subtools.sh hisat

For additional information see the documentation

ml biocontainers hisat2
# paired end alignments
hisat2 -x <index> -1 <forwardseqs.fa> -2 <reverseseqs.fa> -S <output.sam>
# unpaired alignments
hisat2 -x <index> -u <list of files.fa> -S <output.sam>
# SRA access
hisat2 -x <index> --sra-acc <SRA Accession> -S <output.sam>

Parallel Capabilities: Single core default, Multithreading options supported.