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 in | Genome Biology Vol. 16; no. 1; p. 259 |
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| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
BioMed Central
01.12.2015
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| Subjects | |
| Online Access | Get full text |
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| 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 . |
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| AbstractList | 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 .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 . 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 . 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 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 . |
| ArticleNumber | 259 |
| Author | Servant, Nicolas Dekker, Job Lajoie, Bryan R. Varoquaux, Nelle Viara, Eric Vert, Jean-Philippe Barillot, Emmanuel Heard, Edith Chen, Chong-Jian |
| Author_xml | – sequence: 1 givenname: Nicolas surname: Servant fullname: Servant, Nicolas – sequence: 2 givenname: Nelle surname: Varoquaux fullname: Varoquaux, Nelle – sequence: 3 givenname: Bryan R. surname: Lajoie fullname: Lajoie, Bryan R. – sequence: 4 givenname: Eric surname: Viara fullname: Viara, Eric – sequence: 5 givenname: Chong-Jian surname: Chen fullname: Chen, Chong-Jian – sequence: 6 givenname: Jean-Philippe surname: Vert fullname: Vert, Jean-Philippe – sequence: 7 givenname: Edith surname: Heard fullname: Heard, Edith – sequence: 8 givenname: Job surname: Dekker fullname: Dekker, Job – sequence: 9 givenname: Emmanuel surname: Barillot fullname: Barillot, Emmanuel |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26619908$$D View this record in MEDLINE/PubMed https://hal.science/hal-01246671$$DView record in HAL |
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| Copyright | 2015. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Distributed under a Creative Commons Attribution 4.0 International License Servant et al. 2015 |
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| Snippet | 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... |
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| SubjectTerms | 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 |
| Title | HiC-Pro: an optimized and flexible pipeline for Hi-C data processing |
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