Software: SRA-Toolkit
Description
SRA-Toolkit is a collection of tools and libraries for using data in the INSDC Sequence Read Archives
Available Versions
| Unspecified: | 2.11.0-pl5262 |
|---|
Its detailed documentation can be found in https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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