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

by Gonçalves, Sónia , Peacock, Sharon J. , Amato, Roberto , Livett, Rich , Colquhoun, Rachel M. , Nicholls, Samuel M. , Rey, Sara , Rambaut, Andrew , Jackson, Ben , Connor, Thomas R. , Underwood, Anthony , Loman, Nicholas J. , Bull, Matthew J. , Chapman, Michael , Aanensen, David M. , Southgate, Joel , Abu-Dahab, Khalil , Harrison, Ewan M. , Rowe, Will P. M. , Taylor, Ben , Poplawski, Radoslaw , Hill, Verity , O’Toole, Áine

in Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Cloud Computing / COVID-19 / COVID-19 - epidemiology / COVID-19 infection / Editorial / Epidemiological Monitoring / Epidemiology / Evolutionary Biology / genome / Genome, Viral / Genomes / Genomics / Genomics - organization & administration / Human Genetics / Humans / Influenza / infrastructure / Laboratories / Life Sciences / Metadata / Microbial Genetics and Genomics / monitoring / pandemic / Pandemics / Pathogens / Plant Genetics and Genomics / Public health / SARS-CoV-2 - genetics / Sequence Analysis, DNA / Severe acute respiratory syndrome coronavirus 2 / United Kingdom / User-Computer Interface / Whole Genome Sequencing

2021

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

2021

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2021

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Journal Article

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

Gonçalves, Sónia,

Peacock, Sharon J.,

Amato, Roberto,

Livett, Rich,

Colquhoun, Rachel M.,

Nicholls, Samuel M.,

Rey, Sara,

Rambaut, Andrew,

Jackson, Ben,

Connor, Thomas R.,

Underwood, Anthony,

Loman, Nicholas J.,

Bull, Matthew J.,

Chapman, Michael,

Aanensen, David M.,

Southgate, Joel,

Abu-Dahab, Khalil,

Harrison, Ewan M.,

Rowe, Will P. M.,

Taylor, Ben,

Poplawski, Radoslaw,

Hill, Verity,

O’Toole, Áine

2021

Overview

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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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Bioinformatics

/ Biomedical and Life Sciences

/ Cloud Computing

/ COVID-19

/ COVID-19 - epidemiology

/ COVID-19 infection