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Genome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x.

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

Servant N1,2,3, Varoquaux N4,5,6, Lajoie BR7, Viara E8, Chen CJ9,10,11,12,13,14, Vert JP15,16,17, Heard E18,19,20, Dekker J21, Barillot E22,23,24.

Author information

1
Institut Curie, Paris, France. nicolas.servant@curie.fr.
2
INSERM, U900, Paris, France. nicolas.servant@curie.fr.
3
Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. nicolas.servant@curie.fr.
4
Institut Curie, Paris, France. nelle.varoquaux@ensmp.fr.
5
INSERM, U900, Paris, France. nelle.varoquaux@ensmp.fr.
6
Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. nelle.varoquaux@ensmp.fr.
7
Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. Bryan.Lajoie@umassmed.edu.
8
Sysra, Yerres, France. viara@sysra.com.
9
Institut Curie, Paris, France. cchen@annoroad.com.
10
INSERM, U900, Paris, France. cchen@annoroad.com.
11
Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. cchen@annoroad.com.
12
CNRS UMR3215, Paris, France. cchen@annoroad.com.
13
INSERM U934, Paris, France. cchen@annoroad.com.
14
Annoroad Gene Technology Co., Ltd, Beijing, China. cchen@annoroad.com.
15
Institut Curie, Paris, France. Jean-Philippe.Vert@mines.org.
16
INSERM, U900, Paris, France. Jean-Philippe.Vert@mines.org.
17
Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. Jean-Philippe.Vert@mines.org.
18
Institut Curie, Paris, France. edith.heard@curie.fr.
19
CNRS UMR3215, Paris, France. edith.heard@curie.fr.
20
INSERM U934, Paris, France. edith.heard@curie.fr.
21
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.
22
Institut Curie, Paris, France. emmanuel.barillot@curie.fr.
23
INSERM, U900, Paris, France. emmanuel.barillot@curie.fr.
24
Mines ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, Fontainebleau, France. emmanuel.barillot@curie.fr.

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 .

PMID:
26619908
PMCID:
PMC4665391
DOI:
10.1186/s13059-015-0831-x
[Indexed for MEDLINE]
Free PMC Article

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