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

The COVID-19 Genomics UK (COG-UK) Consortium; Samuel M. Nicholls; Radoslaw Poplawski; Matthew J. Bull; Anthony Underwood; Michael Chapman; Khalil Abu-Dahab; Ben Taylor; Rachel M. Colquhoun; Will P.M. Rowe; Ben Jackson; Verity Hill; Áine O’Toole; Sara Rey; Joel Southgate; Roberto Amato; Rich Livett; Sónia Gonçalves; Ewan M. Harrison; Sharon J. Peacock; David M. Aanensen; Andrew Rambaut; Thomas R. Connor; Nicholas J. Loman; Matthew Bashton; Darren Smith; Andrew Nelson; Greg Young; Clare McCann

doi:10.1186/s13059-021-02395-y

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

The COVID-19 Genomics UK (COG-UK) Consortium, Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, Michael Chapman, Khalil Abu-Dahab, Ben Taylor, Rachel M. Colquhoun, Will P.M. Rowe, Ben Jackson, Verity Hill, Áine O’Toole, Sara Rey, Joel Southgate, Roberto Amato, Rich Livett, Sónia Gonçalves, Ewan M. Harrison, Sharon J. PeacockDavid M. Aanensen, Andrew Rambaut, Thomas R. Connor, Nicholas J. Loman^*, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

^*Corresponding author for this work

Research output: Contribution to journal › Editorial › peer-review

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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.

Original language	English
Article number	196
Number of pages	21
Journal	Genome Biology
Volume	22
Issue number	1
Early online date	1 Jul 2021
DOIs	https://doi.org/10.1186/s13059-021-02395-y
Publication status	Published - Dec 2021

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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The COVID-19 Genomics UK (COG-UK) Consortium, Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Colquhoun, R. M., Rowe, W. P. M., Jackson, B., Hill, V., O’Toole, Á., Rey, S., Southgate, J., Amato, R., Livett, R., Gonçalves, S., Harrison, E. M., ... McCann, C. (2021). CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22(1), Article 196. https://doi.org/10.1186/s13059-021-02395-y

@article{e5eac9b32d514f4daf79d36390a2471d,

title = "CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance",

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.",

author = "\{The COVID-19 Genomics UK (COG-UK) Consortium\} and Nicholls, \{Samuel M.\} and Radoslaw Poplawski and Bull, \{Matthew J.\} and Anthony Underwood and Michael Chapman and Khalil Abu-Dahab and Ben Taylor and Colquhoun, \{Rachel M.\} and Rowe, \{Will P.M.\} and Ben Jackson and Verity Hill and {\'A}ine O{\textquoteright}Toole and Sara Rey and Joel Southgate and Roberto Amato and Rich Livett and S{\'o}nia Gon{\c c}alves and Harrison, \{Ewan M.\} and Peacock, \{Sharon J.\} and Aanensen, \{David M.\} and Andrew Rambaut and Connor, \{Thomas R.\} and Loman, \{Nicholas J.\} and Matthew Bashton and Darren Smith and Andrew Nelson and Greg Young and Clare McCann",

note = "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.",

year = "2021",

month = dec,

doi = "10.1186/s13059-021-02395-y",

language = "English",

volume = "22",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central",

number = "1",

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The COVID-19 Genomics UK (COG-UK) Consortium, Nicholls, SM, Poplawski, R, Bull, MJ, Underwood, A, Chapman, M, Abu-Dahab, K, Taylor, B, Colquhoun, RM, Rowe, WPM, Jackson, B, Hill, V, O’Toole, Á, Rey, S, Southgate, J, Amato, R, Livett, R, Gonçalves, S, Harrison, EM, Peacock, SJ, Aanensen, DM, Rambaut, A, Connor, TR, Loman, NJ, Bashton, M , Smith, D , Nelson, A, Young, G & McCann, C 2021, 'CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance', Genome Biology, vol. 22, no. 1, 196. https://doi.org/10.1186/s13059-021-02395-y

TY - JOUR

T1 - CLIMB-COVID

T2 - continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Nicholls, Samuel M.

AU - Poplawski, Radoslaw

AU - Bull, Matthew J.

AU - Underwood, Anthony

AU - Chapman, Michael

AU - Abu-Dahab, Khalil

AU - Taylor, Ben

AU - Colquhoun, Rachel M.

AU - Rowe, Will P.M.

AU - Jackson, Ben

AU - Hill, Verity

AU - O’Toole, Áine

AU - Rey, Sara

AU - Southgate, Joel

AU - Amato, Roberto

AU - Livett, Rich

AU - Gonçalves, Sónia

AU - Harrison, Ewan M.

AU - Peacock, Sharon J.

AU - Aanensen, David M.

AU - Rambaut, Andrew

AU - Connor, Thomas R.

AU - Loman, Nicholas J.

AU - Bashton, Matthew

AU - Smith, Darren

AU - Nelson, Andrew

AU - Young, Greg

AU - McCann, Clare

N1 - 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.

PY - 2021/12

Y1 - 2021/12

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85109127320

U2 - 10.1186/s13059-021-02395-y

DO - 10.1186/s13059-021-02395-y

M3 - Editorial

C2 - 34210356

AN - SCOPUS:85109127320

SN - 1474-7596

VL - 22

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 196

ER -

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

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