# 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](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