Metagenomic toolbox designed for high performances and interpretability. Built with Rust, compatible with Python, and accelerated with multithreading and GPUs.
You can use the project as:
- An executable that processes metagenomic data through the command-line.
- A library that processes metagenomic data in Python or Rust code.
Check the demonstrations out for usage examples.
This project is at an early stage. Planned elements are marked with checkboxes.
You can install stelaro with GPU support, which accelerates the algorithms. This approach is
recommended. Your system needs the OpenCL runtime to build the full project. On Linux, follow this
guide
to install the runtime. On Windows, install the OpenCL runtime from the website of the vendor of
your GPU. After installing the runtime, you may have to place the file libOpenCL.so (Linux) or
OpenCL.lib (Windows) in the directory of the project to build stelaro with GPU support.
Install the full Python package with Maturin by executing:
maturin develop --features opencl
Build the full Rust library and executable by executing:
cargo build --features opencl
You can install stelaro without GPU support. All features will be available, but there will be
no hardware acceleration. This approach is only recommended if your system does not support OpenCL.
Install the CPU-only Python package with Maturin by executing:
maturin develop
Build the CPU-only Rust library and executable by executing:
cargo build
- Create synthetic datasets.
- Stream data from large file collections.
- Process metagenomic data with k-mer and graph-based methods.
- Visualize results
- Measure performances
- Upload the package to PyPI
- Upload the library to crate.io.
demonstrations: Usage examples.documentation: Documentation for Rust and Python.src: Rust source code and OpenCL kernels.stelaro: Python source code.test: Test cases for Rust and Python.
Run the following command to validate the project:
python3 ci.py
This will build all components, run all tests, and validate the coding style.