Attention

WARNING: From 9am on 19th August until 5pm on 2nd September there will be no access to the Stanage HPC cluster.

We will send an email to notify you when Stanage is back online and available for job submission.

Attention

The ShARC HPC cluster was decommissioned on the 30th of November 2023 at 17:00. It is no longer possible for users to access that cluster.

BWA

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

Usage

BWA 0.7.17 can be activated using the module file:

module load apps/bwa/0.7.17/gcc-6.2

The BWA executable is bwa. Type bwa for a list of commands.

Installation notes

BWA 0.7.17 was installed using the install_bwa.sh script; the module file is /usr/local/modulefiles/apps/bwa/0.7.17/gcc-6.2. The installation of BWA 0.7.17 was compiled with GCC 6.2.0.