SRA Toolkit

The Sequence Read Archive (SRA Toolkit) 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*
2.9.0   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.

Publisher/Vendor/Repository and License Type

National Center for Biotechnology Information, Freeware

Usage

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

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