2024
A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK
Colquhoun R, O’Toole Á, Hill V, McCrone J, Yu X, Nicholls S, Poplawski R, Whalley T, Groves N, Ellaby N, Loman N, Connor T, Rambaut A. A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK. Virus Evolution 2024, 10: veae083. PMID: 39493537, PMCID: PMC11529618, DOI: 10.1093/ve/veae083.Peer-Reviewed Original ResearchSARS-CoV-2 genome sequencesSARS-CoV-2 genomeGlobal phylogenetic contextCOVID-19 Genomics UKCOG-UKVariant callingGenome sequencePhylogenetic contextGenomic epidemiologyGenomic surveillanceSARS-CoV-2Public health decision makingHealth decision makingGenomeSequenceSARS-CoV-2 pandemicPhylogeneticallyUnited KingdomQuality controlDecision makingCOVID-19Increasing amount
2021
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O’Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone J, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood S, Aanensen D, Holmes E, Pybus O, Rambaut A. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution 2021, 7: veab064. PMID: 34527285, PMCID: PMC8344591, DOI: 10.1093/ve/veab064.Peer-Reviewed Original ResearchSARS-CoV-2 genomic dataSARS-CoV-2 genome sequencesPhylogenetic assignmentGenome sequenceGenomics communityGenomic dataPangolin toolOutbreak lineageGenomic epidemiologyVirus genomeLineagesTransmission lineagesGenomePangolinsSARS-CoV-2Nomenclature schemeComputational toolsVirusPangoSequenceSevere acute respiratory syndromeAcute respiratory syndrome