BWA-mem2

Description

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.

License

The MIT License.

Usage

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

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

Documentation

Online documentation BWA-mem2 usage.

Homepage

https://github.com/bwa-mem2/bwa-mem2