A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees |
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Authors: | Jakob McBroome Bryan Thornlow Angie S Hinrichs Alexander Kramer Nicola De Maio Nick Goldman David Haussler Russell Corbett-Detig Yatish Turakhia |
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Affiliation: | 1. Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA;2. Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA;3. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom |
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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. |
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Keywords: | COVID-19 SARS-CoV-2 phylogenetics genomic surveillance |
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