oxbow

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)

Learn more from our blog post.

Contributing

Want to contribute? See the contributing guide.