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bioRxiv · 10.1101/2021.12.03.470766

Pandemic-scale phylogenetics

Ye, C.·Thornlow, B.·Kramer, A. M.·McBroome, J.·Hinrichs, A. S.·Corbett-Detig, R.·Turakhia, Y.
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Abstract

1.Phylogenetics has been central to the genomic surveillance, epidemiology and contact tracing efforts during the COVD-19 pandemic. But the massive scale of genomic sequencing has rendered the pre-pandemic tools inadequate for comprehensive phylogenetic analyses. Here, we discuss the phylogenetic package that we developed to address the needs imposed by this pandemic. The package incorporates several pandemic-specific optimization and parallelization techniques and comprises four programs: UShER, matOptimize, RIPPLES and matUtils. Using high-performance computing, UShER and matOptimize maintain and refine daily a massive mutation-annotated phylogenetic tree consisting of all SARS-CoV-2 sequences available in online repositories. With UShER and RIPPLES, individual labs - even with modest compute resources - incorporate newly-sequenced SARS-CoV-2 genomes on this phylogeny and discover evidence for recombination in real-time. With matUtils, they rapidly query and visualize massive SARS-CoV-2 phylogenies. These tools have empowered scientists worldwide to study the SARS-CoV-2 evolution and transmission at an unprecedented scale, resolution and speed.

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Ye, C., Thornlow, B., Kramer, A. M., McBroome, J., Hinrichs, A. S., Corbett-Detig, R., Turakhia, Y.. 2021-12-06. Pandemic-scale phylogenetics. https://doi.org/10.1101/2021.12.03.470766

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