Oxbow is a genomic data I/O library that models and translates next-generation sequencing (NGS) file formats into Apache Arrow representations, opening up genomic data to a richer ecosystem of computational tools.
For example, through oxbow you can access conventional NGS files as in-memory or larger-than-memory data frames in Python, R, and more. Check out the quickstart guide to see how it works.
Read the documentation.
The project is organized as a multi-package monorepo with three main components:
- rs-oxbow (
oxbow/) - A reusable, Rust library providing core parsing and streaming functionality (https://docs.rs/oxbow/) - py-oxbow (
py-oxbow/) - Python bindings built with PyO3/maturin - r-oxbow (
r-oxbow/) - R bindings built with rextendr (minimal, under development)
Data I/O is handled entirely in Rust, with rich high-level features exposed via Python and R.
Learn more from our blog post.
Contributing
Want to contribute? See the contributing guide.