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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Autores principales: Servant, Nicolas, Varoquaux, Nelle, Lajoie, Bryan R., Viara, Eric, Chen, Chong-Jian, Vert, Jean-Philippe, Heard, Edith, Dekker, Job, Barillot, Emmanuel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665391/
https://www.ncbi.nlm.nih.gov/pubmed/26619908
http://dx.doi.org/10.1186/s13059-015-0831-x
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author Servant, Nicolas
Varoquaux, Nelle
Lajoie, Bryan R.
Viara, Eric
Chen, Chong-Jian
Vert, Jean-Philippe
Heard, Edith
Dekker, Job
Barillot, Emmanuel
author_facet Servant, Nicolas
Varoquaux, Nelle
Lajoie, Bryan R.
Viara, Eric
Chen, Chong-Jian
Vert, Jean-Philippe
Heard, Edith
Dekker, Job
Barillot, Emmanuel
author_sort Servant, Nicolas
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0831-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-46653912015-12-02 HiC-Pro: an optimized and flexible pipeline for Hi-C data processing Servant, Nicolas Varoquaux, Nelle Lajoie, Bryan R. Viara, Eric Chen, Chong-Jian Vert, Jean-Philippe Heard, Edith Dekker, Job Barillot, Emmanuel Genome Biol Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0831-x) contains supplementary material, which is available to authorized users. BioMed Central 2015-12-01 2015 /pmc/articles/PMC4665391/ /pubmed/26619908 http://dx.doi.org/10.1186/s13059-015-0831-x Text en © Servant et al. 2015 Open AccessThis 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.
spellingShingle Software
Servant, Nicolas
Varoquaux, Nelle
Lajoie, Bryan R.
Viara, Eric
Chen, Chong-Jian
Vert, Jean-Philippe
Heard, Edith
Dekker, Job
Barillot, Emmanuel
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title_full HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title_fullStr HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title_full_unstemmed HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title_short HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
title_sort hic-pro: an optimized and flexible pipeline for hi-c data processing
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665391/
https://www.ncbi.nlm.nih.gov/pubmed/26619908
http://dx.doi.org/10.1186/s13059-015-0831-x
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