Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology
Bioinformatics | Computational Biology | Genomics | Systems Biology
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 .
Chromosome conformation, Hi-C, Bioinformatics pipeline, Normalization
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Copyright Servant et al. 2015. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
DOI of Published Version
Genome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x. Link to article on publisher's site
Servant, Nicolas; Varoquaux, Nelle; Lajoie, Bryan R.; Viara, Eric; Chen, Chong-Jian; Vert, Jean-Philippe; Heard, Edith; Dekker, Job; and Barillot, Emmanuel, "HiC-Pro: an optimized and flexible pipeline for Hi-C data processing" (2015). Open Access Articles. 2650.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.