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SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

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Title: SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.
Authors: de Bernardi Schneider A; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Su M; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA., Hinrichs AS; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Wang J; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA., Amin H; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA., Bell J; California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA., Wadford DA; California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA., O'Toole Á; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK., Scher E; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK., Perry MD; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA., Turakhia Y; Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA., De Maio N; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, UK., Hughes S; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA., Corbett-Detig R; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
Source: Virus evolution [Virus Evol] 2024 Jan 11; Vol. 10 (1), pp. vead085. Date of Electronic Publication: 2024 Jan 11 (Print Publication: 2024).
Publication Type: Journal Article
Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 101664675 Publication Model: eCollection Cited Medium: Print ISSN: 2057-1577 (Print) Linking ISSN: 20571577 NLM ISO Abbreviation: Virus Evol Subsets: PubMed not MEDLINE
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  Data: SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.
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  Data: <searchLink fieldCode="AU" term="%22de+Bernardi+Schneider+A%22">de Bernardi Schneider A</searchLink>; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.<br /><searchLink fieldCode="AU" term="%22Su+M%22">Su M</searchLink>; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA.<br /><searchLink fieldCode="AU" term="%22Hinrichs+AS%22">Hinrichs AS</searchLink>; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.<br /><searchLink fieldCode="AU" term="%22Wang+J%22">Wang J</searchLink>; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA.<br /><searchLink fieldCode="AU" term="%22Amin+H%22">Amin H</searchLink>; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA.<br /><searchLink fieldCode="AU" term="%22Bell+J%22">Bell J</searchLink>; California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA.<br /><searchLink fieldCode="AU" term="%22Wadford+DA%22">Wadford DA</searchLink>; California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA.<br /><searchLink fieldCode="AU" term="%22O'Toole+Á%22">O'Toole Á</searchLink>; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.<br /><searchLink fieldCode="AU" term="%22Scher+E%22">Scher E</searchLink>; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.<br /><searchLink fieldCode="AU" term="%22Perry+MD%22">Perry MD</searchLink>; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.<br /><searchLink fieldCode="AU" term="%22Turakhia+Y%22">Turakhia Y</searchLink>; Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA.<br /><searchLink fieldCode="AU" term="%22De+Maio+N%22">De Maio N</searchLink>; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, UK.<br /><searchLink fieldCode="AU" term="%22Hughes+S%22">Hughes S</searchLink>; Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA.<br /><searchLink fieldCode="AU" term="%22Corbett-Detig+R%22">Corbett-Detig R</searchLink>; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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  Data: <searchLink fieldCode="JN" term="%22101664675%22">Virus evolution</searchLink> [Virus Evol] 2024 Jan 11; Vol. 10 (1), pp. vead085. <i>Date of Electronic Publication: </i>2024 Jan 11 (<i>Print Publication: </i>2024).
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