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
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/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
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
Documentation
Online documentation BWA-mem2 usage.