EAST

Efficient and accurate detection of topologically associating domains from contact maps. Continuous improvements to high-throughput conformation capture (Hi-C) are revealing richer information about the spatial organization of the chromatin and its role in cellular functions. Several studies have confirmed the existence of structural features of the genome 3D organization that are stable across cell types and conserved across species, called topological associating domains (TADs). The detection of TADs has become a critical step in the analysis of Hi-C data, e.g., to identify enhancer-promoter associations. Here we present East, a novel TAD identification algorithm based on fast 2D convolution of Haar-like features, that is as accurate as the state-of-the-art method based on the directionality index, but 75−80× faster. East is available in the public domain at https://github.com/ucrbioinfo/EAST.

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