Genome Biology (Jul 2021)
CLIMB-COVID: 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,
- Rachel M. Colquhoun,
- Will P. M. Rowe,
- Ben Jackson,
- Verity Hill,
- Áine O’Toole,
- Sara Rey,
- Joel Southgate,
- Roberto Amato,
- Rich Livett,
- Sónia Gonçalves,
- Ewan M. Harrison,
- Sharon J. Peacock,
- David M. Aanensen,
- Andrew Rambaut,
- Thomas R. Connor,
- Nicholas J. Loman,
- The COVID-19 Genomics UK (COG-UK) Consortium
Affiliations
- Samuel M. Nicholls
- Institute of Microbiology and Infection, University of Birmingham
- Radoslaw Poplawski
- Institute of Microbiology and Infection, University of Birmingham
- Matthew J. Bull
- Pathogen Genomics Unit, Public Health Wales NHS Trust
- Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Michael Chapman
- Health Data Research UK Cambridge, Wellcome Genome Campus
- Khalil Abu-Dahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Rachel M. Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh
- Will P. M. Rowe
- Institute of Microbiology and Infection, University of Birmingham
- Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh
- Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh
- Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh
- Sara Rey
- Pathogen Genomics Unit, Public Health Wales NHS Trust
- Joel Southgate
- School of Biosciences, The Sir Martin Evans Building, Cardiff University
- Roberto Amato
- Wellcome Sanger Institute
- Rich Livett
- Wellcome Sanger Institute
- Sónia Gonçalves
- Wellcome Sanger Institute
- Ewan M. Harrison
- Wellcome Sanger Institute
- Sharon J. Peacock
- Department of Medicine, University of Cambridge
- David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh
- Thomas R. Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust
- Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham
- The COVID-19 Genomics UK (COG-UK) Consortium
- DOI
- https://doi.org/10.1186/s13059-021-02395-y
- Journal volume & issue
-
Vol. 22,
no. 1
pp. 1 – 21
Abstract
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.
