CscoreTool: fast Hi-C compartment analysis at high resolution.

Summary: The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, which enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth. Availability and implementation: https://github.com/scoutzxb/CscoreTool. Contact: xzheng@carnegiescience.edu. Supplementary information: Supplementary data are available at Bioinformatics online.