Cargando…
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
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 a...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
BioMed Central
2021
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8247108/ https://www.ncbi.nlm.nih.gov/pubmed/34210356 http://dx.doi.org/10.1186/s13059-021-02395-y |
| _version_ | 1783716454791643136 |
|---|---|
| author | 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. |
| author_facet | 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. |
| author_sort | Nicholls, Samuel M. |
| collection | PubMed |
| description | 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02395-y. |
| format | Online Article Text |
| id | pubmed-8247108 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2021 |
| publisher | BioMed Central |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-82471082021-07-02 CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance 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. Genome Biol Editorial 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02395-y. BioMed Central 2021-07-01 /pmc/articles/PMC8247108/ /pubmed/34210356 http://dx.doi.org/10.1186/s13059-021-02395-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
| spellingShingle | Editorial 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. CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title | CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title_full | CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title_fullStr | CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title_full_unstemmed | CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title_short | CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| title_sort | climb-covid: continuous integration supporting decentralised sequencing for sars-cov-2 genomic surveillance |
| topic | Editorial |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8247108/ https://www.ncbi.nlm.nih.gov/pubmed/34210356 http://dx.doi.org/10.1186/s13059-021-02395-y |
| work_keys_str_mv | AT nichollssamuelm climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT poplawskiradoslaw climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT bullmatthewj climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT underwoodanthony climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT chapmanmichael climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT abudahabkhalil climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT taylorben climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT colquhounrachelm climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT rowewillpm climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT jacksonben climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT hillverity climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT otooleaine climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT reysara climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT southgatejoel climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT amatoroberto climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT livettrich climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT goncalvessonia climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT harrisonewanm climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT peacocksharonj climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT aanensendavidm climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT rambautandrew climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT connorthomasr climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT lomannicholasj climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance AT climbcovidcontinuousintegrationsupportingdecentralisedsequencingforsarscov2genomicsurveillance |