title: HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
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 .
authors.affiliation: Institut Curie, Paris, France. nicolas.servant@curie.fr.|INSERM, U900, Paris, France. nicolas.servant@curie.fr.|Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. nicolas.servant@curie.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.affiliation: Institut Curie, Paris, France. nelle.varoquaux@ensmp.fr.|INSERM, U900, Paris, France. nelle.varoquaux@ensmp.fr.|Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. nelle.varoquaux@ensmp.fr.
authors.forename: Nelle
authors.initials: N
authors.lastname: Varoquaux
authors.affiliation: Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. Bryan.Lajoie@umassmed.edu.
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lajoie
authors.affiliation: Sysra, Yerres, France. viara@sysra.com.
authors.forename: Eric
authors.initials: E
authors.lastname: Viara
authors.affiliation: Institut Curie, Paris, France. cchen@annoroad.com.|INSERM, U900, Paris, France. cchen@annoroad.com.|Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. cchen@annoroad.com.|CNRS UMR3215, Paris, France. cchen@annoroad.com.|INSERM U934, Paris, France. cchen@annoroad.com.|Annoroad Gene Technology Co., Ltd, Beijing, China. cchen@annoroad.com.
authors.forename: Chong-Jian
authors.initials: CJ
authors.lastname: Chen
authors.affiliation: Institut Curie, Paris, France. Jean-Philippe.Vert@mines.org.|INSERM, U900, Paris, France. Jean-Philippe.Vert@mines.org.|Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. Jean-Philippe.Vert@mines.org.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vert
authors.affiliation: Institut Curie, Paris, France. edith.heard@curie.fr.|CNRS UMR3215, Paris, France. edith.heard@curie.fr.|INSERM U934, Paris, France. edith.heard@curie.fr.
authors.forename: Edith
authors.initials: E
authors.lastname: Heard
authors.affiliation: Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. job.dekker@umassmed.edu.
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.affiliation: Institut Curie, Paris, France. emmanuel.barillot@curie.fr.|INSERM, U900, Paris, France. emmanuel.barillot@curie.fr.|Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. emmanuel.barillot@curie.fr.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D000465:Algorithms; D000483:Alleles; D002460:Cell Line; D002875:Chromosomes / Q000737:chemistry*; D023281:Genomics / Q000379:methods*; D006801:Humans; D012984:Software