SRA Toolkit

The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.

Availability and Restrictions

The following versions of SRA Toolkit are available on OSC clusters:

Version Oakley Owens
2.6.3 X* X*
*: Current default version

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

Access

SRA Toolkit is available to all OSC users without restriction.

Usage on Oakley

Set-up

To configure your environment for use of SRA Toolkit, run the following command:   module load sratoolkit. The default version will be loaded. To select a particular SRA Toolkit version, use   module load sratoolkit/version. For example, use  module load sratoolkit/2.6.3 to load SRA Toolkit 2.6.3.

Usage on Owens

Set-up

To configure your environment for use of SRA Toolkit, run the following command:   module load sratoolkit. The default version will be loaded. To select a particular SRA Toolkit version, use   module load sratoolkit/version. For example, use  module load sratoolkit/2.6.3 to load SRA Toolkit 2.6.3.

Further Reading

Service: 
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