SRA Toolkit (sra-tools)

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives (SRA). It includes tools such as prefetch (for downloading) and fasterq-dump (for converting SRA data to FASTQ).

SRA Toolkit (sra-tools)

License

The SRA Toolkit is released into the public domain by the US National Library of Medicine. See the sra-tools repository.

Available

Roihu: 3.3.0 (module sra-tools), via the bio-apps module.

Usage

sra-tools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load sra-tools/3.3.0

Configuration

On first use, configure the toolkit with vdb-config and point its cache to a location with space (for example your project's /scratch) so it does not fill your home directory.

Download an accession and convert it to FASTQ:

prefetch SRR000001
fasterq-dump SRR000001 --threads 8 --outdir fastq

Example batch script

#!/bin/bash
#SBATCH --job-name=fasterq-dump
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load sra-tools/3.3.0

fasterq-dump SRR000001 --threads $SLURM_CPUS_PER_TASK --outdir fastq

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk