Cooler

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A cool place to store your Hi-C

Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.

The cooler file format is an implementation of a genomic matrix data model using HDF5 as the container format. The cooler package includes a suite of command line tools and a Python API to facilitate creating, querying and manipulating cooler files.

To get started:

• Install cooler
• Read the documentation and see the Jupyter Notebook walkthrough.
• cool files from published Hi-C data sets are available here or via s3 (bucket s3://cooler01 --endpoint-url https://usgs2.osn.mghpcc.org --no-sign-request).
• Many more multires (mcool) files are available on the 4DN data portal.

Installation

Install from PyPI using pip.

$ pip install cooler

If you are using conda, you can alternatively install cooler from the bioconda channel.

$ conda install -c conda-forge -c bioconda cooler

Citing

Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. doi: 10.1093/bioinformatics/btz540.

@article{cooler2020,
    author = {Abdennur, Nezar and Mirny, Leonid A},
    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
    journal={Bioinformatics},
    volume={36},
    number={1},
    pages={311--316},
    year={2020},
    doi = {10.1093/bioinformatics/btz540},
    url = {https://doi.org/10.1093/bioinformatics/btz540},
}

Contributing

Interested in contributing to cooler? That's great! To get started, check out the contributing guide.

Related projects

• See other Open2C tools to process Hi-C data (pairtools, distiller) and analyze Hi-C data (cooltools)!
• Visualize your cooler data with HiGlass!
• Check out this list of 3D genomics tools and papers, most of which accept cooler files.

Affiliations and Acknowledgements

• Cooler is an Affiliated Project of NumFOCUS.
• Cooler development has received support from the NIH 4D Nucleome Consortium.
• We are grateful for a storage allocation from NSF's ACCESS Cyberinfrastucture Open Storage Network to host example cooler data.