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qLD: high-performance computation of linkage disequilibrium on CPU and GPU

Theodoris Charalabos, Alachiotis Nikolaos, Low Tze Meng, Pavlidis Pavlos

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URIhttp://purl.tuc.gr/dl/dias/FDCA1154-A621-4ADD-88FB-E1D2B6AE3120-
Identifierhttps://doi.org/10.1109/BIBE50027.2020.00019-
Identifierhttps://ieeexplore.ieee.org/document/9288130/-
Languageen-
Extent8 pagesen
TitleqLD: high-performance computation of linkage disequilibrium on CPU and GPUen
CreatorTheodoris Charalabosen
CreatorΘεοδωρης Χαραλαμποςel
CreatorAlachiotis Nikolaosen
CreatorΑλαχιωτης Νικολαοςel
CreatorLow Tze Mengen
CreatorPavlidis Pavlosen
PublisherInstitute of Electrical and Electronics Engineersen
Content SummaryLinkage disequilibrium (LD) is the non-random association between alleles at different loci. Assessing LD in thousands of genomes and/or millions of single-nucleotide poly-morphisms (SNPs) exhibits excessive time and memory requirements that can potentially hinder future large-scale genomic analyses. To this end, we introduce qLD (quickLD) (https//lgithub.com/StrayLamb2lqLD), a highly optimized open-source software that assesses LD based on Pearson's correlation coefficient. qLD exploits the fact that the computational kernel for calculating LD can be cast in terms of dense linear algebra operations. In addition, the software employs memory-aware techniques to lower memory requirements, and parallel GPU architectures to further shorten analysis times. qLD delivers up to 5x faster processing than the current state-of-the-art software implementation when run on the same CPU, and up to 29x when computation is offloaded to a GPU. Furthermore, the software is designed to quantity allele associations between arbitrarily distant loci in a time-and memory-efficient way, thereby facilitating the evaluation of long-range LD and the detection of co-evolved genes. We showcase qLD on the analysis of 22,554 complete SARS-CoV-2 genomes.en
Type of ItemΔημοσίευση σε Συνέδριοel
Type of ItemConference Publicationen
Licensehttp://creativecommons.org/licenses/by/4.0/en
Date of Item2022-01-24-
Date of Publication2020-
SubjectLinkage disequilibriumen
SubjectSoftwareen
SubjectGPUen
Bibliographic CitationC. Theodoris, N. Alachiotis, T. M. Low and P. Pavlidis, "qLD: high-performance computation of linkage disequilibrium on CPU and GPU," in IEEE Int. Conf. Bioinform. Bioeng. BIBE, 2020, pp. 65-72. doi: 10.1109/BIBE50027.2020.00019.en

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