CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Samuel M. Nicholls, Radoslaw Poplawski, Matthew Bull, Anthony Underwood, Michael Chapman, Khalil Abudahab, Ben Taylor, Rachel 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 Aanensen, Andrew Rambaut, Thomas R. Connor, Nicholas J. Loman
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.