CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

The COVID-19 Genomics UK (COG-UK) Consortium, 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. PeacockDavid M. Aanensen, Andrew Rambaut, Thomas R. Connor, Nicholas J. Loman*, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

*Corresponding author for this work

Research output: Contribution to journalEditorialpeer-review

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.

Original languageEnglish
Article number196
Number of pages21
JournalGenome Biology
Volume22
Issue number1
Early online date1 Jul 2021
DOIs
Publication statusE-pub ahead of print - 1 Jul 2021

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