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Index structure has changed since commit 6743183. Rebuild the Index if you are using a later commit.

# Use precompiled binaries (recommended)
curl -L https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 \
  | tar jxf -
bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index ref.fa
bwa-mem2-2.0pre2_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 MIT license.

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

The usage is exactly same as the original BWA MEM tool. Here is a brief synopsys. Run ./bwa-mem2 for available commands.

# Indexing the reference sequence (Requires 28N GB memory where N is the size of the reference sequence).
./bwa-mem2 index [-p prefix] <in.fasta>
Where 
<in.fasta> is the path to reference sequence fasta file and 
<prefix> is the prefix of the names of the files that store the resultant index. Default is in.fasta.

# Mapping 
# Run "./bwa-mem2 mem" to get all options
./bwa-mem2 mem -t <num_threads> <prefix> <reads.fq/fa> > out.sam
Where <prefix> is the prefix specified when creating the index or the path to the reference fasta file in case no prefix was provided.

Datasets:

Machine details:
Processor: Intel(R) Xeon(R) 8280 CPU @ 2.70GHz
OS: CentOS Linux release 7.6.1810
Memory: 100GB

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.