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 against a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], the HISAT2 developers designed and implemented a graph FM index (GFM). 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 (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. 


Usage on Bridges


To see what versions of HISAT2 are available type

module avail hisat2

To see what other modules are needed, what commands are available and how to get additional help type

module help  hisat2

To use HISAT2, include a command like this in your batch script or interactive session to load the HISAT2 module:

module load hisat2

Be sure you also load any other modules needed, as listed by the module help hisat2 command.


User Information

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Technical questions:

Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.