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dc.contributor.authorHerruzo-Ruiz, José Manuel 
dc.contributor.authorGonzález-Navarro, Sonia 
dc.contributor.authorIbáñez, Pablo
dc.contributor.authorViñals, Victor
dc.contributor.authorAlastruey-Benedé, Jesús
dc.contributor.authorÓscar, Plata
dc.date.accessioned2024-01-30T12:44:50Z
dc.date.available2024-01-30T12:44:50Z
dc.date.issued2020-07-01
dc.identifier.urihttps://hdl.handle.net/10630/29410
dc.description.abstractFM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95 percent of the peak random access bandwidth limit when executed on the KNL and almost all of the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature.es_ES
dc.description.sponsorshipTIN2016-80920-R, PID2019-105396RB-I00, UMA18-FEDERJA-197es_ES
dc.language.isoenges_ES
dc.publisherIEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,es_ES
dc.rightsinfo:eu-repo/semantics/openAccesses_ES
dc.subjectBioinformáticaes_ES
dc.subject.otherFM-indexes_ES
dc.subject.otherIntel Xeon Phi Knights-Landinges_ES
dc.subject.otherShort-read alignmentes_ES
dc.subject.otherHigh-bandwidth memoryes_ES
dc.titleAccelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processores_ES
dc.typeinfo:eu-repo/semantics/articlees_ES
dc.centroE.T.S.I. Informáticaes_ES
dc.identifier.doihttps://doi.org/10.1109/TCBB.2018.2884701
dc.type.hasVersioninfo:eu-repo/semantics/acceptedVersiones_ES


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