HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas ServantINSERM, U900, Paris, France. [email protected]Nelle VaroquauxINSERM, U900, Paris, France. [email protected]Bryan R. LajoieProgram in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. [email protected]Eric ViaraSysra, Yerres, France. [email protected]Chong-Jian ChenAnnoroad Gene Technology Co., Ltd, Beijing, China. [email protected]Jean‐Philippe VertINSERM, U900, Paris, France. [email protected]Édith HeardCNRS UMR3215, Paris, France. [email protected]Job DekkerHoward Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA. [email protected]Emmanuel BarillotINSERM, U900, Paris, France. [email protected]
2015en
ABI
Аннотация
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 .
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