CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.
Samuel M NichollsRadoslaw PoplawskiMatthew J BullAnthony UnderwoodMichael ChapmanKhalil Abu-DahabBen TaylorRachel M ColquhounWill P M RoweBen JacksonVerity HillÁine O'TooleSara ReyJoel SouthgateRoberto AmatoRich LivettSónia GonçalvesEwan M HarrisonSharon J PeacockDavid M AanensenAndrew RambautThomas Richard ConnorNicholas J Lomannull nullPublished in: Genome biology (2021)
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.