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PARamrfinder: detecting allele-specific DNA methylation on multicore clusters
dc.contributor.author | Fernández Fraga, Alejandro | |
dc.contributor.author | González-Domínguez, Jorge | |
dc.contributor.author | Martín, María J. | |
dc.date.accessioned | 2024-04-01T10:47:56Z | |
dc.date.available | 2024-04-01T10:47:56Z | |
dc.date.issued | 2024-01 | |
dc.identifier.citation | Fernández-Fraga, A., González-Domínguez, J. & Martín, M.J. PARamrfinder: detecting allele-specific DNA methylation on multicore clusters. J Supercomput (2024). https://doi.org/10.1007/s11227-024-05939-8 | es_ES |
dc.identifier.uri | http://hdl.handle.net/2183/36028 | |
dc.description | Financiado para publicación en acceso aberto: CRUE-CSIC | es_ES |
dc.description.abstract | [Abstract]: The discovery of Allele-Specific Methylation (ASM) is an important research field in biology as it regulates genomic imprinting, which has been identified as the cause of some genetic diseases. Nevertheless, the high computational cost of the bioinformatic tools developed for this purpose prevents their application to large-scale datasets. Hence, much faster tools are required to further progress in this research field. In this work we present PARamrfinder, a parallel tool that applies a statistical model to identify ASM in data from high-throughput short-read bisulfite sequencing. It is based on the state-of-the-art sequential tool amrfinder, which is able to detect ASM at regional level from Bisulfite Sequencing (BS-Seq) experiments in the absence of Single Nucleotide Polymorphism information. PARamrfinder provides the same Allelically Methylated Regions as amrfinder but at significantly reduced runtime thanks to exploiting the compute capabilities of common multicore CPU clusters and MPI RMA operations to attain an efficient dynamic workload balance. As an example, our tool is up to 567 times faster for real data experiments on a cluster with 8 nodes, each one containing two 16-core processors. The source code of PARamrfinder, as well as a reference manual, is available at https://github.com/UDC-GAC/PARamrfinder. | es_ES |
dc.description.sponsorship | Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was supported by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 and PID2022-136435NB-I00 / AEI / 10.13039/501100011033), PID2022 also funded by “ERDF A way of making Europe”. It was also supported by the Ministry of Universities of Spain under grant FPU21/03408, and by Xunta de Galicia and FEDER funds (Centro de Investigación de Galicia accreditation 2019–2022 and Consolidation Program of Competitive Reference Groups, under Grants ED431G 2019/01 and ED431C 2021/30, respectively). | es_ES |
dc.description.sponsorship | Xunta de Galicia; ED431G 2019/01 | es_ES |
dc.description.sponsorship | Xunta de Galicia; ED431C 2021/30 | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | Springer | es_ES |
dc.relation | info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-104184RB-I00/ES/DESAFIOS ACTUALES EN HPC: ARQUITECTURAS, SOFTWARE Y APLICACIONES | es_ES |
dc.relation | info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-136435NB-I00/ES/ARQUITECTURAS, FRAMEWORKS Y APLICACIONES DE LA COMPUTACION DE ALTAS PRESTACIONES | es_ES |
dc.relation | info:eu-repo/grantAgreement/MECD/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/FPU21%2F03408/ES/ | es_ES |
dc.relation.uri | https://doi.org/10.1007/s11227-024-05939-8 | es_ES |
dc.rights | Attribution 4.0 International (CC BY) | es_ES |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/es/ | * |
dc.subject | Allele-specific methylation | es_ES |
dc.subject | High performance computing | es_ES |
dc.subject | MPI | es_ES |
dc.subject | OpenMP | es_ES |
dc.subject | RMA | es_ES |
dc.subject | Dynamic load balancing | es_ES |
dc.title | PARamrfinder: detecting allele-specific DNA methylation on multicore clusters | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.rights.access | info:eu-repo/semantics/openAccess | es_ES |
UDC.journalTitle | T he Journal of Supercomputing | es_ES |
UDC.volume | 2024 | es_ES |
dc.identifier.doi | 10.1007/s11227-024-05939-8 |
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