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, hit.strand, hit.cigar_string)
- 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 withmeth=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.
1 maintainer
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