On September 22nd, OSC switched to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.


HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.

Availability and Restrictions


HISAT2 is available on the Owens Cluster. The versions currently available at OSC are:

Version Owens Pitzer
2.1.0 X* X*
* Current Default Version

You can use module spider hisat2 to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


HISAT2 is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

https://ccb.jhu.edu/software/hisat2, Open source


Usage on Owens and Pitzer


To configure your enviorment for use of HISAT2, use command module load hisat2. This will load the default version.

Further Reading

Fields of Science: