Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. Mustache is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, Mustache recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, Mustache enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache.