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.
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Nicholls, S., Poplawski, R., Bull, M., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Colquhoun, R., Rowe, W., Jackson, B., Hill, V., O'Toole, Á., Rey, S., Southgate, J., Amato, R., Livett, R., Gonçalves, S., Harrison, E., Peacock, S., Aanensen, D., Rambaut, A., Connor, T., Loman, N. & The COVID-19 Genomics UK (COG-UK) Consortium 2021, 'CLIMB-COVID: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance', Genome Biology, 22, article no: 196. https://doi.org/10.1186/s13059-021-02395-y