SRAToolKit-Sapelo2

Category

BioInformatics

Program On

Sapelo2

Version

3.0.1, 3.0.3

Author / Distributor

Please see https://github.com/ncbi/sra-tools

Description

The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The Sequence Read Archives (SRA) store raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. The SRA-Toolkit includes the following tools:

Command	Description
fastq-dump	Convert SRA data into fastq format
prefetch	Allows command-line downloading of SRA, dbGaP, and ADSP data
sam-dump	Convert SRA data to sam format
sra-pileup	Generate pileup statistics on aligned SRA data
vdb-config	Display and modify VDB configuration information
vdb-decrypt	Decrypt non-SRA dbGaP data ("phenotype data")
abi-dump	Convert SRA data into ABI format (csfasta / qual)
illumina-dump	Convert SRA data into Illumina native formats (qseq, etc.)
sff-dump	Convert SRA data to sff format
sra-stat	Generate statistics about SRA data (quality distribution, etc.)
vdb-dump	Output the native VDB format of SRA data.
vdb-encrypt	Encrypt non-SRA dbGaP data ("phenotype data")
vdb-validate	Validate the integrity of downloaded SRA data

Downloading SRA Data

The last version of this application is at /apps/eb/SRA-Toolkit/3.0.3-gompi-2022a

To use this version, please load the module with

ml SRA-Toolkit/3.0.3-gompi-2022a

You can download SRA data to local directory with the prefetch tool. This program downloads Runs (sequence files in the compressed SRA format) and all additional data necessary to convert the Run from the SRA format to a more commonly used format. You can search for a dataset using the search bar at the top of the SRA homepage. https://www.ncbi.nlm.nih.gov/sra Once you find a dataset you would like to download, search for the "Run number" in the table towards the bottom of the webpage for that dataset. Then create the folder where prefetch will deposit your files. This needs to be an empty folder. It is recommended that you download data into your scratch directory since there is plenty of space there.

Next, run the command:

vdb-config --interactive

This will open a screen where you operate the buttons by pressing the letter highlighted in red, or by pressing the tab-key until the wanted button is reached and then pressing the space- or the enter-key. Make sure there is an X by the "Enable Remote Access" option on the MAIN tab, and X by the "enable local file-caching" option in the CACHE tab. Then set the "location of user-repository" to the empty folder you created. In the following image the data will be downloaded to /scratch/keekov/prefetchData. These settings are stored in a file called user-settings.mkfg in a hidden directory called .ncbi in the top level of your home directory.

Then press "s" or navigate to the save button and press enter to save. Then press "x" or navigate to the exit button and press enter to exit. Now you can start the data download by running the command prefetch followed by the run number. For example the following downloads the dataset SRR390728.

prefetch SRR390728

For more information about the prefetch command refer to the documentation

Running Program

You can now run other SRA-Tools on the SRA data you've downloaded. Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo please see the Lmod page.

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=SRA-ToolsExample
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=fastq-dump.%j.out
#SBATCH --error=fastq-dump.%j.err

cd $SLURM_SUBMIT_DIR
ml SRA-Toolkit/3.0.3-gompi-2022a
fastq-dump -X 5 -Z /scratch/keekov/SRR390728.sra #You should use the directory you selected in the vdb-config step above

Documentation

Please see https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc for the documentation of each tool.

System

64-bit Linux