bwa-mem3

A faster, more correct, drop-in replacement for bwa mem and bwa-mem2.

If you align short reads with bwa or bwa-mem2 today, bwa-mem3 will give you the same answers — only quicker, with fewer rough edges, and with first-class support for things you used to need a wrapper script for.

Why bwa-mem3

• Drop in, go faster. Same algorithm, same outputs, same flags as bwa-mem2 — but consolidated mapping speedups, a memory-bounded index builder, batched header ingestion, and a tuned allocator add up to measurable wall-clock wins on real workloads.
• Methylation in one binary. A --meth flag turns bwa-mem3 into a drop-in replacement for the entire bwameth.py pipeline. No Python, no inline conversion script, no separate post-processing step. One bwa-mem3 index --meth ref.fa, one bwa-mem3 mem --meth ref.fa R1.fq R2.fq, done — header collapsed, tags emitted, chimeras flagged.
• Stage the index once, align many. A bwa-mem3 shm subcommand pins the FM-index in shared memory so back-to-back runs on the same host skip the 28 GB read every time.
• Correctness fixes upstream hasn’t merged yet. Tabs in -R, 151+ bp reads, AVX-512 mate-rescue, kswv score2 plateau across NEON/AVX2/AVX-512BW, mem_sam_pe proper-pair flag — every fix tracked back to the upstream PR or issue that found it.
• Architecture-aware out of the box. SSE4.1, SSE4.2, AVX, AVX2, AVX-512BW, and ARM64/NEON. A multi-binary launcher picks the right one for your CPU.

Get started in 30 seconds

git clone --recursive https://github.com/fg-labs/bwa-mem3
cd bwa-mem3 && make
./bwa-mem3 index ref.fa
./bwa-mem3 mem -t 16 ref.fa R1.fq.gz R2.fq.gz \
  | samtools sort -@ 8 -o out.bam

Tip — Emit BAM directly

For production pipelines, add --bam=0 to skip the SAM text round-trip entirely. See Best Practices: Output format.

Where to start

• Installation — Build from source (Bioconda is on the way).
• Quick start: align paired-end FASTQs — Two commands to your first alignment.
• Quick start: methylation — The one-binary bwameth.py replacement, in two commands.
• Best Practices — The five things that actually move the needle for production runs.
• What’s different from bwa-mem2 — Every fix and feature, with upstream cross-references.

What’s in this book

• Getting Started — Install and run your first alignment.
• User Guide — Indexing, alignment, output, threading, allocator notes.
• Performance — Where the speed comes from and how to get more.
• Best Practices — Build, run, and deploy recommendations.
• CLI Reference — Every flag, auto-captured from --help.
• Methylation Reference — --meth mode in full.
• What’s Different from bwa-mem2 — The full changelog, by category.
• Developer Guide — Build matrix, SIMD dispatch, regression tests, contributing.
• Related Projects — bwa-mem3-bench, bwa-mem3-rs, fgumi, bwa-mem2 upstream.
• Reference — Glossary, citation, license, changelog.

bwa-mem3 is a derivative of bwa-mem2 maintained by Fulcrum Genomics. MIT licensed. See License and Citation.