Dissemin is shutting down on January 1st, 2025

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BioMed Central, Genome Biology, 1(16), 2015

DOI: 10.1186/s13059-015-0831-x

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

Journal article published in 2015 by Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert ORCID, Edith Heard, Job Dekker, Emmanuel Barillot
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 .