On September 22nd OSC will be switching 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.

HTSlib

HTSlib is a C library used for reading and writing high-throughput sequencing data. HTSlib is the core library used by SAMtools. HTSlib also provides the bgziphtsfile, and tabix utilities.

Availability and Restrictions

Versions

The versions of HTSlib currently available at OSC are:

Version Owens
1.6 X*
* Current Default Version

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

Access

HTSlib is available to all OSC users.

Publisher/Vendor/Repository and License Type

Genome Research Ltd., Open source

Usage

Usage on Owens

Set-up

To set up the environment for HTSlib on the OSC clusters, use the command:

module load htslib/1.6

Further Reading

Supercomputer: