HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas Servant(Inserm), Nelle Varoquaux(Inserm), Bryan R. Lajoie(University of Massachusetts Chan Medical School), Eric Viara(SYSTRA (France)), Chong-Jian Chen(Centre National de la Recherche Scientifique), Jean‐Philippe Vert(Inserm), Édith Heard(Centre National de la Recherche Scientifique), Job Dekker(Howard Hughes Medical Institute), Emmanuel Barillot(Inserm)
Cited by 2,849Open Access
Abstract
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro .