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The next version of bwa-mem (WIP; not recommended for production uses at the moment)
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Makefile added MIT license Sep 9, 2019 added a simple README May 21, 2019 Added citation May 27, 2019

Getting Started

# Use precompiled binaries (recommended)
curl -L \
  | 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
cd 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.

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