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

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

doi:10.1186/s13059-021-02395-y

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

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. AanensenAndrew Rambaut, Thomas R. Connor, Nicholas J. Loman

School of Biological Sciences

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

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
Number of pages	21
Journal	Genome Biology
Volume	22
Issue number	196
DOIs	https://doi.org/10.1186/s13059-021-02395-y
Publication status	Published - 1 Jul 2021

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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., Peacock, S. J., ... Loman, N. J. (2021). CLIMB-COVID: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22(196). https://doi.org/10.1186/s13059-021-02395-y

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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 = "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.}",

year = "2021",

month = jul,

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

language = "English",

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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 2021, 'CLIMB-COVID: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance', Genome Biology, vol. 22, no. 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 - 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.

PY - 2021/7/1

Y1 - 2021/7/1

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.

U2 - 10.1186/s13059-021-02395-y

DO - 10.1186/s13059-021-02395-y

M3 - Editorial

SN - 1465-6906

VL - 22

JO - Genome Biology

JF - Genome Biology

IS - 196

ER -

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

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