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Pandemic-scale phylogenetics

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 pack...

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Autores principales: Ye, Cheng, Thornlow, Bryan, Kramer, Alexander, McBroome, Jakob, Hinrichs, Angie, Corbett-Detig, Russell, Turakhia, Yatish
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8679213/
https://www.ncbi.nlm.nih.gov/pubmed/34927180
http://dx.doi.org/10.1101/2021.12.03.470766
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author Ye, Cheng
Thornlow, Bryan
Kramer, Alexander
McBroome, Jakob
Hinrichs, Angie
Corbett-Detig, Russell
Turakhia, Yatish
author_facet Ye, Cheng
Thornlow, Bryan
Kramer, Alexander
McBroome, Jakob
Hinrichs, Angie
Corbett-Detig, Russell
Turakhia, Yatish
author_sort Ye, Cheng
collection PubMed
description 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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spelling pubmed-86792132021-12-18 Pandemic-scale phylogenetics Ye, Cheng Thornlow, Bryan Kramer, Alexander McBroome, Jakob Hinrichs, Angie Corbett-Detig, Russell Turakhia, Yatish bioRxiv Article 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. Cold Spring Harbor Laboratory 2021-12-06 /pmc/articles/PMC8679213/ /pubmed/34927180 http://dx.doi.org/10.1101/2021.12.03.470766 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Ye, Cheng
Thornlow, Bryan
Kramer, Alexander
McBroome, Jakob
Hinrichs, Angie
Corbett-Detig, Russell
Turakhia, Yatish
Pandemic-scale phylogenetics
title Pandemic-scale phylogenetics
title_full Pandemic-scale phylogenetics
title_fullStr Pandemic-scale phylogenetics
title_full_unstemmed Pandemic-scale phylogenetics
title_short Pandemic-scale phylogenetics
title_sort pandemic-scale phylogenetics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8679213/
https://www.ncbi.nlm.nih.gov/pubmed/34927180
http://dx.doi.org/10.1101/2021.12.03.470766
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