bwa-mem3 is a short-read aligner derived from bwa-mem2, carrying correctness fixes, performance improvements, and new features (methylation alignment, shared-memory index, mimalloc allocator) maintained by Fulcrum Genomics.
Full documentation: https://bwa-mem3.readthedocs.io
git clone --recursive https://github.com/fg-labs/bwa-mem3.git
cd bwa-mem3
make
./bwa-mem3 version- bwa-mem3-bench — benchmarking harness across CPU architectures
- bwa-mem3-rs — Rust bindings for bwa-mem3
- fgumi — UMI-aware consensus and deduplication
- bwa-mem2 — upstream project
MIT. See the License page in the docs.
Please cite the bwa-mem2 paper (Vasimuddin Md et al., IPDPS 2019). See the Citation page for BibTeX.
File issues and pull requests on fg-labs/bwa-mem3.