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

Nicholls Samuel M.,Poplawski Radoslaw, Bull Matthew J., Oxford Big Data Institute, Old Road Campus,Chapman Michael, Oxford Big Data Institute, Old Road Campus, Oxford Big Data Institute, Old Road Campus, Colquhoun Rachel M., Rowe Will P. M.,Jackson Ben,Hill Verity, O’Toole Áine, Rey Sara, Southgate Joel,Amato Roberto, Livett Rich,Gonçalves Sónia, University of Cambridge, Peacock Sharon J., Oxford Big Data Institute, Old Road Campus,Rambaut Andrew, Quadram Institute,Loman Nicholas J.

Genome Biology（2021）

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摘要

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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