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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean‐Philippe Vert, Édith Heard, Job Dekker, Emmanuel Barillot

Genome biology · 2015 · 2.9K citations · 22 references

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TL;DR

HiC‑Pro is an optimized, flexible pipeline that processes Hi‑C data from raw reads to normalized contact maps. It maps reads, identifies valid ligation products, performs quality control, and generates intra‑ and inter‑chromosomal contact maps using a fast iterative correction algorithm and a memory‑efficient format, and can build allele‑specific maps from phased genotype data. We applied HiC‑Pro to various Hi‑C datasets, demonstrating its ability to process large data quickly, and the source code and documentation are available at the provided GitHub link.

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 .