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

被引：1632

作者：

Servant, Nicolas ^{[1
,2
,3
]}

Varoquaux, Nelle ^{[1
,2
,3
]}

Lajoie, Bryan R. ^{[4
]}

Viara, Eric ^{[5
]}

Chen, Chong-Jian ^{[1
,2
,3
,6
,7
,8
]}

Vert, Jean-Philippe ^{[1
,2
,3
]}

Heard, Edith ^{[1
,6
,7
]}

Dekker, Job ^{[9
]}

Barillot, Emmanuel ^{[1
,2
,3
]}

机构：

[1] Inst Curie, Paris, France

[2] INSERM, U900, Paris, France

[3] PSL Res Univ, Mines ParisTech, CBIO Ctr Computat Biol, Fontainebleau, France

[4] Univ Massachusetts, Sch Med, Dept Biochem & Mol Pharmacol, Program Syst Biol, Worcester, MA USA

[5] Sysra, Yerres, France

[6] CNRS, UMR3215, Paris, France

[7] INSERM, U934, Paris, France

[8] Annoroad Gene Technol Co Ltd, Beijing, Peoples R China

[9] Univ Massachusetts, Sch Med, Howard Hughes Med Inst, Dept Biochem & Mol Pharmacol,Program Syst Biol, Worcester, MA 01605 USA

来源：

GENOME BIOLOGY | 2015年 / 16卷

关键词：

Chromosome conformation; Hi-C; Bioinformatics pipeline; Normalization; HUMAN GENOME; CHROMOSOME; ORGANIZATION; INTERACTOME; PRINCIPLES; BIASES; MAP;

D O I：

10.1186/s13059-015-0831-x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

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