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., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22 (1). p. 196. ISSN 1474-760X
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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.
| Item Type: | Article |
|---|---|
| Additional Information: | Funding Information: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. CLIMB is funded by the Medical Research Council (MRC) through grant MR/L015080/1. The authors would like to thank the Birmingham Environment for Academic Research (BEAR) at the University of Birmingham for supporting the deployment of this project. SN would like to thank Nadim Rahman (European Bioinformatics Institute) for assistance with the ENA API and INSDC submissions and Gunter Bach (GISAID) for implementing our suggestions into the GISAID API. Matthew Bashton, Andrew Nelson, Darren Smith, Greg Young are members of the COVID-19 Genomics UK (COG-UK) consortium. |
| Subjects: | B900 Others in Subjects allied to Medicine C100 Biology C500 Microbiology C900 Others in Biological Sciences |
| Department: | Faculties > Health and Life Sciences > Applied Sciences |
| Depositing User: | Rachel Branson |
| Date Deposited: | 08 Sep 2021 14:11 |
| Last Modified: | 08 Sep 2021 14:15 |
| URI: | http://nrl.northumbria.ac.uk/id/eprint/47108 |
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