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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot

ABSTRACT

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 . More... »

PAGES

259

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-015-0831-x

DOI

http://dx.doi.org/10.1186/s13059-015-0831-x

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036760229

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26619908


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