pybwa
Python bindings for bwa, the Burrows-Wheeler Aligner.
Pybwa provides native Python access to bwa's indexing and alignment algorithms, returning
pysam AlignedSegment objects for downstream analysis.
Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with pybwa and beyond.
Quick Start
Align reads with bwa mem
bwa mem is the recommended algorithm for reads longer than ~70bp (Illumina, etc.).
from pybwa import BwaMem
mem = BwaMem(prefix="/path/to/genome.fasta")
for recs in mem.align(queries=["CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA"]):
for rec in recs:
print(rec)
Align short reads with bwa aln
bwa aln is designed for short reads (<100bp, e.g. Illumina).
from pybwa import BwaAln
aln = BwaAln(prefix="/path/to/genome.fasta")
for rec in aln.align(queries=["GATTACA"]):
print(rec)
Reuse an index across aligners
Load a BwaIndex once and pass it to multiple aligners to avoid reloading:
from pybwa import BwaIndex, BwaAln, BwaMem
index = BwaIndex(prefix="/path/to/genome.fasta")
aln = BwaAln(index=index)
mem = BwaMem(index=index)
Installation
Install with pip install pybwa or conda install -c bioconda pybwa.
Requires Python 3.10+
Documentation
See the full documentation on pybwa.readthedocs.org.
Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with pybwa and beyond.
Metadata
Release files for pybwa 2.3.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| pybwa-2.3.2.tar.gz | 7.9 MB | With provenance | Details for pybwa-2.3.2.tar.gz |
Built distributions (wheels)
Total release size: 296.5 MB
Release files / pybwa-2.3.2.tar.gz
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| Size | 7.9 MB |
| Tags | Source |
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