HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs (Sirén et al. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first implementation. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.

Version: 2.0.4 (MARCONI) 2.2.1 (G100)

Availability: GALILEO100, MARCONI

Target: all

Official web site: https://ccb.jhu.edu/software/hisat2/

Related Commands:

To load the application you should run:

module load profile/bioinf
module load autoload hisat2

HINT: Some genomic indexes have been already prepared and located under the $HISAT2_INDEXES env variable

Help and Documentation:

You can find documentation on the system, with the command

module help hisat2

The manual is on the web at the original home page (http://daehwankimlab.github.io/hisat2/download/)


CINECA consultants can be reached through the address: superc@cineca.it