SRA-Toolkit

Introduction

SRA-Toolkit is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Its detailed documentation can be found in https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc.

Versions

  • 2.11.0-pl5262

Commands

  • abi-dump

  • align-cache

  • align-info

  • bam-load

  • cache-mgr

  • cg-load

  • fasterq-dump

  • fasterq-dump-orig

  • fastq-dump

  • fastq-dump-orig

  • illumina-dump

  • kar

  • kdbmeta

  • kget

  • latf-load

  • md5cp

  • prefetch

  • prefetch-orig

  • rcexplain

  • read-filter-redact

  • sam-dump

  • sam-dump-orig

  • sff-dump

  • sra-pileup

  • sra-pileup-orig

  • sra-sort

  • sra-sort-cg

  • sra-stat

  • srapath

  • srapath-orig

  • sratools

  • test-sra

  • vdb-config

  • vdb-copy

  • vdb-diff

  • vdb-dump

  • vdb-encrypt

  • vdb-lock

  • vdb-passwd

  • vdb-unlock

  • vdb-validate

Module

You can load the modules by:

module load biocontainers
module load sra-tools/2.11.0-pl5262

Configuring SRA-Toolkit

Users can config SRA-Toolkit by the command vdb-config. For example, the below command set up the current working directory for downloading:

vdb-config --prefetch-to-cwd

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run SRA-Toolkit on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=SRA-Toolkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers sra-tools/2.11.0-pl5262

vdb-config --prefetch-to-cwd # The data will be downloaded to the current working directory.
prefetch SRR11941281
fastq-dump --split-3 SRR11941281/SRR11941281.sra