cvlr: finding heterogeneously methylated genomic regions using ONT reads

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  • dc.contributor.author Raineri, Emanuele
  • dc.contributor.author Alberola i Pla, Mariona
  • dc.contributor.author Dabad, Marc
  • dc.contributor.author Heath, Simon
  • dc.date.accessioned 2023-06-20T06:24:38Z
  • dc.date.available 2023-06-20T06:24:38Z
  • dc.date.issued 2023
  • dc.description.abstract Summary: Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous methylation. Our software can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads. Availability and implementation: https://github.com/EmanueleRaineri/cvlr. Contact: simon.heath@cnag.crg.eu. Supplementary information: Supplementary data are available at Bioinformatics Advances online.
  • dc.description.sponsorship This work was supported by a Spanish Plan Nacional grant [project: PGC2018-099640-B-I00]. Furthermore, we acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, of the Centro de Excelencia Severo Ochoa and of the CERCA Programme/Generalitat de Catalunya. We also acknowledge support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III of the Generalitat de Catalunya through Departament de Salut and Departament d’Universitats i Recerca. We also acknowledge the Co-financing with funds from the European Regional Development Fund by the Spanish Ministry of Science and Innovation corresponding to the Programa Operativo FEDER Plurirregional de España (POPE) 2014–2020 and by the Departament d’Universitats i Recerca of the Generalitat de Catalunya corresponding to the Programa Operatiu FEDER de Catalunya 2014–2020.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Raineri E, Alberola I Pla M, Dabad M, Heath S. cvlr: finding heterogeneously methylated genomic regions using ONT reads. Bioinform Adv. 2023 Jan 23;3(1):vbac101. DOI: 10.1093/bioadv/vbac101
  • dc.identifier.doi http://dx.doi.org/10.1093/bioadv/vbac101
  • dc.identifier.issn 2635-0041
  • dc.identifier.uri http://hdl.handle.net/10230/57257
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Bioinform Adv. 2023 Jan 23;3(1):vbac101
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-099640-B-I00
  • dc.rights © The Author(s) 2023. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Genome analysis
  • dc.title cvlr: finding heterogeneously methylated genomic regions using ONT reads
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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