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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Nicholls, Samuel M 
Poplawski, Radoslaw 
Bull, Matthew J 
Underwood, Anthony 
Chapman, Michael 

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.

Description

Keywords

COVID-19, Cloud Computing, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, SARS-CoV-2, Sequence Analysis, DNA, United Kingdom, User-Computer Interface, Whole Genome Sequencing

Journal Title

Genome Biology

Conference Name

Journal ISSN

1474-7596
1474-760X

Volume Title

22

Publisher

BioMed Central
Sponsorship
MRC (MC_PC_19027)
UK Research and Innovation (MC_PC_19027)
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.