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

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

Authors :
McBroome, Jakob
Thornlow, Bryan
Hinrichs, Angie S
Kramer, Alexander
Maio, Nicola De
Goldman, Nick
Haussler, David
Corbett-Detig, Russell
Turakhia, Yatish
Source :
Molecular Biology & Evolution; Dec2021, Vol. 38 Issue 12, p5819-5824, 6p
Publication Year :
2021

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%5fSARS-CoV-2/ and https://github.com/yatisht/usher , respectively. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
07374038
Volume :
38
Issue :
12
Database :
Complementary Index
Journal :
Molecular Biology & Evolution
Publication Type :
Academic Journal
Accession number :
154512835
Full Text :
https://doi.org/10.1093/molbev/msab264