Single-cell Hi-C research currently lacks an efficient, easy to use and shareable data storage format. Recent studies have used a variety of sub-optimal solutions: publishing raw data only, text-based interaction matrices, or reusing established Hi-C storage formats for single interaction matrices. These approaches are storage and pre-processing intensive, require long labour time and are often error-prone.


The single-cell cooler file format (scool) provides an efficient, user-friendly and storage-saving approach for single-cell Hi-C data. It is a flavour of the established cooler format and guarantees stable API support.

Availability and implementation

The single-cell cooler format is part of the cooler file format as of API version 0.8.9. It is available via pip, conda and github:

Supplementary information

Supplementary data are available at Bioinformatics online.

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