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

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...

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Published inGenome Biology Vol. 16; no. 1; p. 259
Main Authors Servant, Nicolas, Varoquaux, Nelle, Lajoie, Bryan R., Viara, Eric, Chen, Chong-Jian, Vert, Jean-Philippe, Heard, Edith, Dekker, Job, Barillot, Emmanuel
Format Journal Article
LanguageEnglish
Published England BioMed Central 01.12.2015
Subjects
Algorithms
Alleles
Bioinformatics
Cell Line
Chromosomes
Chromosomes - chemistry
data collection
Data processing
Datasets
Deoxyribonucleic acid
DNA
Enzymes
Gene mapping
genome
Genomes
Genomics - methods
genotype
Genotypes
Humans
Life Sciences
Pipelines
Quantitative Methods
Software
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Summary: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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PMCID: PMC4665391
ISSN:1474-760X
1474-7596
1465-6906
1474-760X
DOI:10.1186/s13059-015-0831-x