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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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).

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

More information