# Use precompiled binaries (recommended) curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre1/bwa-mem2-2.0pre1_x64-linux.tar.bz2 \ | tar jxf - bwa-mem2-2.0pre1_x64-linux/bwa-mem2 index ref.fa bwa-mem2-2.0pre1_x64-linux/bwa-mem2 mem ref.fa read1.fq read2.fq > out.sam # Compile from source (not recommended for general users) git clone https://github.com/bwa-mem2/bwa-mem2 cd bwa-mem2 make ./bwa-mem2
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~80% faster.
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 GPL3 license and is likely to be changed to a permissive license in the near future.
For general users, it is recommended to use the precompiled binaries from the
release page. These binaries were compiled with the Intel compiler and
runs faster than gcc-compiled binaries. The precompiled binaries also
indirectly support CPU dispatch. The
bwa-mem2 binary can automatically choose
the most efficient implementation based on the SIMD instruction set available
on the running machine. Precompiled binaries were generated on a CentOS6
machine using the following command line:
make CXX=icpc multi
Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.