A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

被引：57

作者：

McBroome, Jakob ^{[1
,2
]}

Thornlow, Bryan ^{[1
,2
]}

Hinrichs, Angie S. ^{[2
]}

Kramer, Alexander ^{[1
,2
]}

De Maio, Nicola ^{[3
]}

Goldman, Nick ^{[3
]}

Haussler, David ^{[1
,2
]}

Corbett-Detig, Russell ^{[1
,2
]}

Turakhia, Yatish ^{[1
,2
]}

机构：

[1] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

[2] Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA

[3] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Genome Campus, Cambridge, England

来源：

MOLECULAR BIOLOGY AND EVOLUTION | 2021年 / 38卷 / 12期

关键词：

COVID-19; SARS-CoV-2; phylogenetics; genomic surveillance; IMMUNODEFICIENCY-VIRUS TYPE-1;

D O I：

10.1093/molbev/msab264

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 Glade and Pango lineage labels at Glade 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://gihub.com/yatisht/usher, respectively.

引用

页码：5819 / 5824

页数：6

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