HiCRep.py : Fast comparison of Hi-C contact matrices in Python.

MOTIVATION: Hi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to asses experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high resolution Hi-C data or on large single-cell Hi-C datasets.
RESULTS: We introduce a Python implementation of HiCRep and demonstrate that it is much faster and consume much less memory than the existing R implementation. Furthermore, we give examples of HiCRep's ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data. AVAILABILITY: HiCRep.py and its documentation are available with a GPL license at https://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer. SUPPLEMENTARY INFORMATION: Supplementary methods and results are included in an appendix at Bioinformatics online.