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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.
Nicholls, Samuel M; Poplawski, Radoslaw; Bull, Matthew J; Underwood, Anthony; Chapman, Michael; Abu-Dahab, Khalil; Taylor, Ben; Colquhoun, Rachel M; Rowe, Will P M; Jackson, Ben; Hill, Verity; O'Toole, Áine; Rey, Sara; Southgate, Joel; Amato, Roberto; Livett, Rich; Gonçalves, Sónia; Harrison, Ewan M; Peacock, Sharon J; Aanensen, David M; Rambaut, Andrew; Connor, Thomas R; Loman, Nicholas J.
Afiliação
  • Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Poplawski R; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Bull MJ; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
  • Underwood A; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
  • Chapman M; Oxford Big Data Institute, Old Road Campus, Oxford, UK.
  • Abu-Dahab K; Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton, UK.
  • Taylor B; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
  • Colquhoun RM; Oxford Big Data Institute, Old Road Campus, Oxford, UK.
  • Rowe WPM; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
  • Jackson B; Oxford Big Data Institute, Old Road Campus, Oxford, UK.
  • Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • O'Toole Á; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Rey S; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Southgate J; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Amato R; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Livett R; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
  • Gonçalves S; School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK.
  • Harrison EM; Wellcome Sanger Institute, Hinxton, UK.
  • Peacock SJ; Wellcome Sanger Institute, Hinxton, UK.
  • Aanensen DM; Wellcome Sanger Institute, Hinxton, UK.
  • Rambaut A; Wellcome Sanger Institute, Hinxton, UK.
  • Connor TR; Department of Medicine, University of Cambridge, Cambridge, UK.
  • Loman NJ; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Genome Biol ; 22(1): 196, 2021 07 01.
Article em En | MEDLINE | ID: mdl-34210356
ABSTRACT
In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genômica / Computação em Nuvem / SARS-CoV-2 Idioma: En Ano de publicação: 2021 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Genômica / Computação em Nuvem / SARS-CoV-2 Idioma: En Ano de publicação: 2021 Tipo de documento: Article