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 | Owens | Pitzer |
|---|---|---|
| 2.6.3 | X | |
| 2.9.0 | X* | |
| 2.9.1 | X* | |
| 2.9.6 | X |
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. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
National Center for Biotechnology Information, Freeware
Usage
Usage on Owens
Set-up
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
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.Download SRA Data
At OSC, you can use Aspera to facilitate SRA data download. For example, prefetch with SRA accession
$ module load sratoolkit/2.9.x $ prefetch -v SRR390728 $USE_ASPERA
The default download path is in your home directory ~/ncbi. For example, you can find the SRA file SRR390728.sra in ~/ncbi/sra and the resource files in ~/ncbi/refseq. Then you can run other SRA tools, e.g. fastq-dump on computing nodes. Here is a job script example:
#PBS -N use_fastq_dump #PBS -j oe #PBS -l walltime=0:10:0 #PBS -l nodes=1:ppn=1 cd $PBS_O_WORKDIR module load sratoolkit/2.9.0 module list fastq-dump -X 5 -Z SRR390728
However, our Home Directory file system is not suitable for heavy computation. If the SRA file is large, you can consider the following two options for better performance.
Copy SRA file to $TMPDIR
Use the script above as an example, copy the SRA data to $TMPDIR before calling fastq-dump:
cp ~/ncbi/sra/SRR390728.sra $TMPDIR cd $TMPDIR fastq-dump -X 5 -Z ./SRR390728
Change default download path to a faster file system, i.e. /fs/scratch
You can change the default download path for SRA data to our scratch file system with one of following two approaches. For example, /fs/scratch/PAS1234/johndoe/ncbi:
### Approach 1.
#
$ mkdir -p ~/.ncbi
$ echo '/repository/user/main/public/root = "/fs/scratch/PAS1234/johndoe/ncbi"' > ~/.ncbi/user-settings.mkfg
$ module load sratoolkit/2.9.x
$ prefetch -v SRR390728 $USE_ASPERA
### Approach 2. CAUTION: make sure no working data in ~/ncbi
#
$ rm -rf ~/ncbi/*
$ rmdir ~/ncbi
$ ln -s /fs/scratch/PAS1234/johndoe/ncbi ~/ncbi
$ module load sratoolkit/2.9.x
$ prefetch -v SRR390728 $USE_ASPERA
Then your SRA data are saved in /fs/scratch/PAS1234/johndoe/ncbi and SRA tools will load data from this directory.
