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 | Pitzer |
|---|---|---|---|
| 2.6.3 | X* | X* | |
| 2.9.0 | X | ||
| 2.9.1 | 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.
Usage on Pitzer
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/2.9.1 to load SRA Toolkit 2.9.1.Further Reading
Service:
Fields of Science: