SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization

High-throughput chromosome conformation capture (Hi-C) technology captures spatial interactions of DNA sequences into matrices, and software tools are developed to identify topologically associating domains (TADs) from the Hi-C matrices. With structural information theory, SuperTAD adopted a dynamic programming approach to find the TAD hierarchy with minimal structural entropy. However, the algorithm suffers from high time complexity. To accelerate this algorithm, we design and implement an approximation algorithm with a theoretical performance guarantee. We implemented a package, SuperTAD-Fast. Using Hi-C matrices and simulated data, we demonstrated that SuperTAD-Fast achieved great runtime improvement compared with SuperTAD. SuperTAD-Fast shows high consistency and significant enrichment of structural proteins from Hi-C data of human cell lines in comparison with the existing six hierarchical TADs detecting methods.