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.

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02395-y.