bwa-mem2

bwa-mem2 is the next version of the bwa mem algorithm in BWA. It produces alignments identical to bwa mem but runs faster, at the cost of a larger index. It is used for aligning short reads against a large reference genome.

• bwa-mem2
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source under the MIT License.

Available

• Roihu: 2.3, via the bio-apps module.

Usage

bwa-mem2 is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the bwa-mem2 module:

module load bio-apps/v202603
module load bwa-mem2/2.3

First index the reference genome (this needs more memory and disk than BWA):

bwa-mem2 index reference.fa

Then align reads:

bwa-mem2 mem -t 8 reference.fa read1.fq read2.fq > aln.sam

Example batch script

#!/bin/bash
#SBATCH --job-name=bwa-mem2
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G

module load bio-apps/v202603
module load bwa-mem2/2.3

bwa-mem2 mem -t $SLURM_CPUS_PER_TASK reference.fa read1.fq read2.fq > aln.sam

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• bwa-mem2 GitHub repository

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