Accelerated Pangenome Graph Queries =================================== Pollen is a nascent project to accelerate queries on pangenomic graphs. We are designing a graph-manipulating DSL that exposes functionality that pangenomicists care about. Our DSL will support graph queries in the vein of the [odgi][] project. We will compile programs written in this DSL into fast query code. Eventually, we aim to generate custom hardware accelerators for these queries via the [Calyx][] compiler. There are several things in this repository: * [mygfa](./mygfa), a simple Python library for parsing, processing, and emitting [GFA][] files. See [its documentation][mygfa-docs]. * [slow_odgi](./slow_odgi), a reference implementation of several GFA queries from the [odgi][] tool using `mygfa`. * [FlatGFA](./flatgfa), an experimental fast binary format for representing and analyzing GFA files. There are also [Python bindings](./flatgfa-py) for this library; check out [their documentation][flatgfa-py-docs]. * A proof-of-concept Calyx-based [hardware accelerator generator](./pollen_py) for a single GFA query (`odgi depth`) and a data generator for this hardware. [calyx]: https://calyxir.org [odgi]: https://odgi.readthedocs.io/en/latest/ [gfa]: https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md [flatgfa-py-docs]: https://cucapra.github.io/pollen/flatgfa/ `mygfa` and `slow_odgi` ----------------------- The `mygfa` library is an extremely simple Python library for representing (and parsing and emitting) GFA files. It emphasizes clarity over efficiency. Use `pip install mygfa` to get started, and read the [API documentation][mygfa-docs] for details. Similarly, `slow_odgi` is a set of GFA analyses based on `mygfa`; it's meant to act as a *reference implementation* of the much faster functionality in [odgi][]. Check out [the slow_odgi README](slow_odgi/) for more details. To set up both of them from this repository, try using [uv][]: $ uv run slow_odgi --help Or, alternatively, you can set up and activate the environment manually: $ uv sync $ source .venv/bin/activate $ slow_odgi --help [uv]: https://github.com/astral-sh/uv [mygfa-docs]: http://cucapra.github.io/pollen/mygfa/ FlatGFA ------- [FlatGFA](./flatgfa) is an efficient representation for GFA files. It is implemented in Rust and available with [Python bindings](./flatgfa-py). The latter is [on PyPI][flatgfa-pypi], so you can get started with: $ pip install flatgfa Then read the [API documentation][flatgfa-py-docs] to see what's available. Or see [the included example](./flatgfa-py/example.py) for a synopsis. [flatgfa-pypi]: https://pypi.org/project/flatgfa/ Credits ------- This is a project of the [Capra][] lab at Cornell. The license is [MIT][]. [capra]: https://capra.cs.cornell.edu [mit]: https://choosealicense.com/licenses/mit/

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