minibwa 0.1.0

Python bindings for minibwa

minibwa

Python bindings for minibwa, a minimal BWA-style short- and long-read aligner. Built on the Rust minibwa crate via PyO3; the alignment runs in native code with the GIL released.

Install

pip install minibwa

Quick start

import minibwa

# Build an index from a FASTA (writes <prefix>.l2b and <prefix>.mbw), then load it.
minibwa.Index.build("ref.fa", "ref")
idx = minibwa.Index.load("ref")

opts = minibwa.Opts()
for hit in minibwa.map(idx, opts, "read1", "ACGTACGT..."):
    print(hit.contig, hit.ref_start, hit.ref_end, "-" if hit.reverse else "+", hit.cigar)

• Paired-end: minibwa.map_pair(idx, opts, n1, s1, n2, s2)
• Batched (higher throughput): minibwa.map_many(idx, opts, names, seqs)
• Methylation (bisulfite): pass meth=minibwa.Meth.C2T / Meth.G2A (build/load the index with meth=True)

See the project repository for the full API and documentation.

License

MIT. The package vendors and links minibwa (MIT) and libsais (Apache-2.0); see the repository's THIRD-PARTY.md for full notices.