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dc.contributor.authorServant, Nicolas
dc.contributor.authorVaroquaux, Nelle
dc.contributor.authorLajoie, Bryan R.
dc.contributor.authorViara, Eric
dc.contributor.authorChen, Chong-Jian
dc.contributor.authorVert, Jean-Philippe
dc.contributor.authorHeard, Edith
dc.contributor.authorDekker, Job
dc.contributor.authorBarillot, Emmanuel
dc.date2022-08-11T08:09:44.000
dc.date.accessioned2022-08-23T16:41:16Z
dc.date.available2022-08-23T16:41:16Z
dc.date.issued2015-12-01
dc.date.submitted2015-12-23
dc.identifier.citationGenome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x. <a href="http://dx.doi.org/10.1186/s13059-015-0831-x">Link to article on publisher's site</a>
dc.identifier.issn1474-7596 (Linking)
dc.identifier.doi10.1186/s13059-015-0831-x
dc.identifier.pmid26619908
dc.identifier.urihttp://hdl.handle.net/20.500.14038/39852
dc.description.abstractHiC-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 .
dc.language.isoen_US
dc.relation<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=26619908&dopt=Abstract">Link to Article in PubMed</a>
dc.rightsCopyright Servant et al. 2015. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a>), 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 (<a href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</a>) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectChromosome conformation
dc.subjectHi-C
dc.subjectBioinformatics pipeline
dc.subjectNormalization
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.subjectGenomics
dc.subjectSystems Biology
dc.titleHiC-Pro: an optimized and flexible pipeline for Hi-C data processing
dc.typeJournal Article
dc.source.journaltitleGenome biology
dc.source.volume16
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=3654&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/2650
dc.identifier.contextkey7972031
refterms.dateFOA2022-08-23T16:41:17Z
html.description.abstract<p>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 .</p>
dc.identifier.submissionpathoapubs/2650
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Systems Biology
dc.source.pages259


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Copyright Servant et al. 2015. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a>), 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 (<a href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</a>) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as Copyright Servant et al. 2015. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<a href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</a>), 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 (<a href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</a>) applies to the data made available in this article, unless otherwise stated.