Scalable neighbour search and alignment with uvaia

de Oliveira Martins, Leonardo, Mather, Alison E. and Page, Andrew J. (2024) Scalable neighbour search and alignment with uvaia. PeerJ, 12. ISSN 2167-8359

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Abstract

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

Item Type:	Article
Additional Information:	Data Availability Statement: The following information was supplied regarding data availability: Sequence read data and consensus genomes from COGUK are available at the European Nucleotide Archive: PRJEB37886. All data are also available at GitHub: https://github.com/quadram-institute-bioscience/uvaia. Video tutorials are available at Youtube: https://www.youtube.com/playlist?list=PLPZ2aSS2ApqoU6-FCd2H035uJHnLu9fTL. Funding information: This research was funded by the Biological Sciences Research Council (BBSRC) Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain), also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Uncontrolled Keywords:	alignment,covid-19,distance,genomics,neighbour search,phylogenetics,sars-cov-2,sequencing,snp,neuroscience(all),biochemistry, genetics and molecular biology(all),agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/2800
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	23 Oct 2024 15:30
Last Modified:	23 Oct 2024 15:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/97151
DOI:	10.7717/PEERJ.16890

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