A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees. (1st September 2021)

• Record Type: Journal Article
• Authors: McBroome, Jakob; Thornlow, Bryan; Hinrichs, Angie S; Kramer, Alexander; De Maio, Nicola; Goldman, Nick; Haussler, David; Corbett-Detig, Russell; Turakhia, Yatish
• Editors: Lu, Jian
• Is Part Of: Molecular biology and evolution. Volume 38:Number 12(2021)
• Page Start: 5819
• Page End: 5824
• Publication Date: 2021-09-01
• Subjects: COVID-19 -- SARS-CoV-2 phylogenetics -- genomic surveillance; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msab264
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations, as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834, 521 sequences and provides a comprehensive view of the virus' evolutionary history using public data. We also present matUtils—a command-line utility for rapidly querying, interpreting, and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.