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MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Samuel M Nicholls; Radoslaw Poplawski; Matthew J Bull; Anthony Underwood; Michael Chapman; Khalil Abu-Dahab; Ben Taylor; Ben Jackson; Sara Rey; Roberto Amato; Rich Livett; Sonia Goncalves; Ewan M Harrison; Sharon J Peacock; David M Aanensen; Andrew Rambaut; Thomas R Connor; Nicholas J Loman; - The COVID-19 Genomics UK Consortium (COG-UK).
  • Samuel M Nicholls; Institute of Microbiology and Infection, University of Birmingham, Birmingham
  • Radoslaw Poplawski; Institute of Microbiology and Infection, University of Birmingham, Birmingham
  • Matthew J Bull; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff
  • Anthony Underwood; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton
  • Michael Chapman; Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton
  • Khalil Abu-Dahab; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton
  • Ben Taylor; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton
  • Ben Jackson; University of Edinburgh
  • Sara Rey; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff
  • Roberto Amato; Wellcome Sanger Institute, Hinxton
  • Rich Livett; Wellcome Sanger Institute, Hinxton
  • Sonia Goncalves; Wellcome Sanger Institute, Hinxton
  • Ewan M Harrison; Wellcome Sanger Institute, Hinxton
  • Sharon J Peacock; University of Cambridge, Department of Medicine, Cambridge
  • David M Aanensen; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton
  • Andrew Rambaut; University of Edinburgh
  • Thomas R Connor; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff
  • Nicholas J Loman; Institute of Microbiology and Infection, University of Birmingham, Birmingham
  • - The COVID-19 Genomics UK Consortium (COG-UK); -
Preprint in English | bioRxiv | ID: ppbiorxiv-328328
ABSTRACT
Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data. In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing 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 Majora, 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. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date.
Full text: Available Collection: Preprints Database: bioRxiv Type of study: Screening study Language: English Year: 2020 Document Type: Preprint

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Full text: Available Collection: Preprints Database: bioRxiv Type of study: Screening study Language: English Year: 2020 Document Type: Preprint