SRA-Toolkit

Owned by Simon Alexander
Last updated: Nov 14, 2022
1 min read
1 Overview | 2 Using | 2.1 Multicore

Overview

  • The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

Using

Use the module name sratoolkitto discover versions available and to load the application.

First Time Use: Configuration: If using for the first time, please run vdb-config -i, further instructions can be found on the Quick Toolkit Configuration page.

Multicore

The sratoolkit has a number of commands that can be used across multiple threads/cores, run the command with the -h option for further details.

For example, running fasterq-dump -h you can look up the -e|--threads options for further details.