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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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