HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Inserm · Université Paris Sciences et Lettres · +10 more institutions
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 .
Citation impact
- FWCI
- 25.90
- Percentile
- 100%
- References
- 24
Authors
9- NSNicolas ServantCorresponding
Inserm, Université Paris Sciences et Lettres, École Nationale Supérieure des Mines de Paris, Institut Curie
- NVNelle Varoquaux
Inserm, École Nationale Supérieure des Mines de Paris, Institut Curie
- BRBryan R. Lajoie
University of Massachusetts Chan Medical School
- EVEric Viara
SYSTRA (France)
- CCChong-Jian Chen
Centre National de la Recherche Scientifique, Inserm, Annoroad Gene Technology (China), Archéologie et Philologie d’Orient et d’Occident, Génétique et biologie du développement, École Nationale Supérieure des Mines de Paris, Institut Curie
Topics & keywords
- Pipeline (software)
- Documentation
- Computer science
- Process (computing)
- Source code
- Data mining
- Programming language