hisat2

Summary

• Module Name: hisat2

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: http://www.ccb.jhu.edu/software/hisat/index.shtml

Software Description

From the HISAT webpage: “HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low (~4.3GB for the human genome).”

General Linux

To load this module for use in a Linux environment, you can run the command:

module load hisat2

Depending on where you are working, there may be more than one version of hisat2 available. To see which modules are available for loading you can run:

module avail hisat2