qLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU

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

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

1 Citation (Scopus)

Abstract

Linkage 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.
Original languageEnglish
Title of host publication2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)
Place of PublicationPiscataway, NJ
PublisherIEEE
ISBN (Electronic)978-1-7281-9574-2
ISBN (Print)978-1-7281-9575-9
DOIs
Publication statusPublished - 2020
Event20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020 - Cincinnati, United States
Duration: 26 Oct 202028 Oct 2020
Conference number: 20

Publication series

NameProceedings IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
PublisherIEEE
Volume2020
ISSN (Print)2159-5410
ISSN (Electronic)2471-7819

Conference

Conference20th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2020
Abbreviated titleBIBE
CountryUnited States
CityCincinnati
Period26/10/2028/10/20

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