sra-toolkit

Version:

3.0.0

Category:

bio

Cluster:

Loki

Author / Distributor

https://github.com/ncbi/sra-tools

Description

The SRA Toolkit is a collection of command-line utilities and libraries for accessing and working with the NCBI Sequence Read Archive (SRA). It enables users to download, convert, and process sequencing data stored in the SRA in formats such as FASTQ, SAM/BAM, and SRA.

Version 3.0.0 introduces improvements in:

  • Compatibility with modern secure HTTPS endpoints

  • Memory-efficient streaming of large datasets

  • Updated accession resolution and configuration handling

  • Improved support for fasterq-dump and vdb-dump tools

Documentation

Common commands:
----------------
prefetch SRRXXXXXXX
    Download SRA data by accession

fasterq-dump SRRXXXXXXX
    Convert SRA to FASTQ (faster than fastq-dump)

fastq-dump --split-files SRRXXXXXXX
    Legacy FASTQ conversion tool

vdb-dump SRRXXXXXXX
    Dump database table contents to stdout

vdb-validate SRRXXXXXXX
    Validate local SRA file integrity

Configuration:
--------------
vdb-config --interactive
    Launch interactive configuration tool

Help:
  $ fasterq-dump --help
  $ vdb-config --help
  $ prefetch --help

Examples/Usage

  • Load the module:

$ module load bio/SRA-Toolkit/3.0.0

  • Download SRA accession:

$ prefetch SRR12345678

  • Convert to FASTQ:

$ fasterq-dump SRR12345678 -O ./fastq/

  • View contents of an SRA file:

$ vdb-dump SRR12345678 | less

  • Validate a file:

$ vdb-validate SRR12345678

  • Configure settings:

$ vdb-config --interactive

  • Unload the module:

$ module unload bio/SRA-Toolkit/3.0.0

Installation

Source code is obtained from NCBI SRA Toolkit