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dc.contributor.authorMartínez Pérez, Héctor
dc.contributor.authorBarrachina Mir, Sergio
dc.contributor.authorCastillo Catalán, Maribel
dc.contributor.authorTárraga, Joaquín
dc.contributor.authorMedina, Ignacio
dc.contributor.authorDopazo, Joaquín
dc.contributor.authorQuintana Ortí, Enrique S.
dc.date.accessioned2018-06-22T09:36:30Z
dc.date.available2018-06-22T09:36:30Z
dc.date.issued2016-06
dc.identifier.citationMARTÍNEZ, Héctor, et al. A framework for genomic sequencing on clusters of multicore and manycore processors. The International Journal of High Performance Computing Applications, 2016, 1094342016653243.ca_CA
dc.identifier.urihttp://hdl.handle.net/10234/175290
dc.description.abstractThe advances in genomic sequencing during the past few years have motivated the development of fast and reliable software for DNA/RNA sequencing on current high performance architectures. Most of these efforts target multicore processors, only a few can also exploit graphics processing units, and a much smaller set will run in clusters equipped with any of these multi-threaded architecture technologies. Furthermore, the examples that can be used on clusters today are all strongly coupled with a particular aligner. In this paper we introduce an alignment framework that can be leveraged to coordinately run any “single-node” aligner, taking advantage of the resources of a cluster without having to modify any portion of the original software. The key to our transparent migration lies in hiding the complexity associated with the multi-node execution (such as coordinating the processes running in the cluster nodes) inside the generic-aligner framework. Moreover, following the design and operation in our Message Passing Interface (MPI) version of HPG Aligner RNA BWT, we organize the framework into two stages in order to be able to execute different aligners in each one of them. With this configuration, for example, the first stage can ideally apply a fast aligner to accelerate the process, while the second one can be tuned to act as a refinement stage that further improves the global alignment process with little cost.ca_CA
dc.format.extent14 P.ca_CA
dc.format.mimetypeapplication/pdfca_CA
dc.language.isoengca_CA
dc.publisherSageca_CA
dc.rightsCopyright © 2018 by SAGE Publicationca_CA
dc.subjectgenomic sequencingca_CA
dc.subjectDNA-seqca_CA
dc.subjectRNA-seqca_CA
dc.subjecthigh performance computingca_CA
dc.subjectclustersca_CA
dc.subjectmulti-threaded architecturesca_CA
dc.titleA framework for genomic sequencing on clusters of multicore and manycore processorsca_CA
dc.typeinfo:eu-repo/semantics/articleca_CA
dc.identifier.doihttps://doi.org/10.1177/1094342016653243
dc.relation.projectIDUniversity Jaume I, MINECO/CICYT (grant numbers TIN2011-23283 and TIN2014-53495-R) and FEDERca_CA
dc.rights.accessRightsinfo:eu-repo/semantics/openAccessca_CA
dc.relation.publisherVersionhttp://journals.sagepub.com/doi/abs/10.1177/1094342016653243ca_CA
dc.type.versioninfo:eu-repo/semantics/acceptedVersionca_CA


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