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BWA-mem2 is the next version of the BWA-mem algorithm in BWA. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.


The MIT License.


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of bwa-mem2 and load default version of bwa-mem2 as

module avail bwa-mem2/ # list available modules
module load bwa-mem2   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail bwa-mem2

and choose explicit version you want to use.

bwa-mem2 version   # Will show the software version
bwa-mem2 index -p <prefix_name> <in_reference.fasta>
bwa-mem2 mem <prefix_name> <reads_1.fq/fa> <reads_2.fq/fa> -t $PBS_NUM_PPN > out.sam


Online documentation BWA-mem2 usage.