StripePy: fast and robust characterization of architectural stripes.

ABSTRACT:

Motivation

Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair. Despite their importance, few tools exist for automatic stripe detection.

Results

We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C. StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community.

Availability and implementation

StripePy is released to the public as an open-source, MIT-licensed Python application. StripePy source code is hosted on GitHub at https://github.com/pauls

SUBMITTER: Raffo A 

PROVIDER: S-EPMC12215313 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature