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 original bwa was developed by Heng Li (@lh3). Performance enhancement in bwa-mem2 was primarily done by Vasimuddin Md (@yuk12) and Sanchit Misra (@sanchit-misra) from Parallel Computing Lab, Intel. bwa-mem2 is distributed under the MIT license.

• Latest version: 2.2.1
• Added: August, 2024
• Link: https://github.com/bwa-mem2/bwa-mem2

See versions which are available:

$ module avail bwa-mem2

Load one version into your environment and run it:

$ module load bwa-mem2/2.2.1
$ bwa-mem2

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2
$ tar xf bwa-mem2-2.2.1_x64-linux.tar.bz2 
$ sudo mkdir -p /export/apps/bwa-mem2/2.2.1/bin
$ sudo cp bwa-mem2-2.2.1_x64-linux/* /export/apps/bwa-mem2/2.2.1/bin