SRAToolKit-Sapelo2

Category

BioInformatics

Program On

Sapelo2

Version

2.9.6-1,2.10.8,2.11.1

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:

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

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. 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 /home/keeko/prefetchData.

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.

fetch 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.

#!/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
SRA-Toolkit/2.11.1-centos_linux64
fastq-dump -X 5 -Z /home/keekov/SRR390728.sra

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