Sra-tools

Introduction

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/sra-tools
Home page: https://github.com/ncbi/sra-tools

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.11.0-pl5262

BELL

2.11.0-pl5262

GAUTSCHI

2.11.0-pl5262

NEGISHI

2.11.0-pl5262

SCHOLAR

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

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-tools on our clusters:

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

module --force purge
module biocontainers sra-tools

# Your sra-tools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sra-tools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers sra-tools

# Your sra-tools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sra-tools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers sra-tools

# Your sra-tools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sra-tools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers sra-tools

# Your sra-tools workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sra-tools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers sra-tools

# Your sra-tools workflow...