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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing #MMPMID26619908
Servant N; Varoquaux N; Lajoie BR; Viara E; Chen CJ; Vert JP; Heard E; Dekker J; Barillot E
Genome Biol 2015[]; 16 (ä): ä PMID26619908show ga
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.Electronic supplementary material: The online version of this article (doi:10.1186/s13059-015-0831-x) contains supplementary material, which is available to authorized users.