Installation

Bioconda (coming soon)

A Bioconda package for bwa-mem3 is in preparation. Once published, installation will be:

conda install -c bioconda bwa-mem3

This will be the recommended path for most users. Check back here or watch the fg-labs/bwa-mem3 repository for the announcement.

Build from source

Until the Bioconda package is available, build from source using the steps below.

Prerequisites

A C++17 compiler (GCC 8+ or Clang 7+)
GNU make
Rust toolchain (for cargo install of mdbook tools, not required for the aligner itself)
Git (for submodule checkout)

Clone and build

git clone --recursive https://github.com/fg-labs/bwa-mem3
cd bwa-mem3
make

The --recursive flag is required. bwa-mem3 vendors several libraries (mimalloc, sse2neon, and others) as git submodules. A shallow or non-recursive clone will fail to compile.

Warning — Shallow clone submodule pitfall

If you cloned without --recursive, initialize the submodules before running make:
git submodule update --init --recursive
Forgetting this step is the most common source of build failures.

Target architecture

By default, make builds a general-purpose binary that runs on any supported CPU. For maximum performance, specify the architecture that matches your deployment target:

Flag	Requires	Notes
`make`	SSE4.1 or better (x86), any (ARM)	Default; selects best dispatch at runtime on x86
`make arch=avx2`	AVX2 (e.g. Haswell, Zen 2)	Recommended for modern x86 servers
`make arch=avx512bw`	AVX-512BW (e.g. Skylake-X, Ice Lake, Sapphire Rapids)	Maximum x86 performance
`make arch=arm64`	Apple Silicon / AWS Graviton	NEON-vectorized build

See Performance — SIMD dispatch matrix for the full matrix of which kernels are vectorized under each target.

Memory allocator (mimalloc)

bwa-mem3 bundles mimalloc and links it into every binary by default. mimalloc reduces allocator contention under high thread counts and lowers wall-clock time on multi-threaded alignment runs.

To build without mimalloc, pass USE_MIMALLOC=0:

make USE_MIMALLOC=0

See User Guide — Memory allocator for details on how mimalloc is linked on Linux versus macOS and when opting out is appropriate.

Smoke test

After building, run the smoke test to confirm the binary works and report which allocator is active:

./bwa-mem3 version

Expected output (with mimalloc):

bwa-mem3-0.1.0-pre-12-gabcdef1
mimalloc 3.x.x

If the mimalloc line is absent, the build linked the system allocator (expected when USE_MIMALLOC=0 was passed or when the vendor submodule was not initialized).

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