Introduction

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 .

Publications

  1. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
    Cite this
    Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E, 2015-12-01 - Genome biology

Credits

  1. Nicolas Servant
    Developer

    Mines ParisTech, PSL-Research University, France

  2. Nelle Varoquaux
    Developer

    Mines ParisTech, PSL-Research University, France

  3. Bryan R Lajoie
    Developer

    Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology

  4. Eric Viara
    Developer

    Sysra, Yerres

  5. Chong-Jian Chen
    Developer

    Annoroad Gene Technology Co., Ltd

  6. Jean-Philippe Vert
    Developer

    Mines ParisTech, PSL-Research University, France

  7. Edith Heard
    Developer

    INSERM U934, Paris

  8. Job Dekker
    Developer

    Howard Hughes Medical Institute, Program in Systems Biology

  9. Emmanuel Barillot
    Investigator

    Mines ParisTech, PSL-Research University, France

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Summary
AccessionBT006824
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionFrance
Submitted ByEmmanuel Barillot