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

Nicholls, S. M.; Poplawski, R.; Bull, M. J.; Underwood, A.; Chapman, M.; Abu-Dahab, K.; Taylor, B.; Jackson, B.; Rey, S.; Amato, R.; Livett, R.; Goncalves, S.; Harrison, E. M.; Peacock, S. J.; Aanensen, D. M.; Rambaut, A.; Connor, T. R.; Loman, N. J.; The COVID-19 Genomics UK Consortium (COG-UK),

doi:10.1101/2020.10.06.328328

bioRxiv · 10.1101/2020.10.06.328328

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

Nicholls, S. M.·Poplawski, R.·Bull, M. J.·Underwood, A.·Chapman, M.·Abu-Dahab, K.·Taylor, B.·Jackson, B.·Rey, S.·Amato, R.·Livett, R.·Goncalves, S.·Harrison, E. M.·Peacock, S. J.·Aanensen, D. M.·Rambaut, A.·Connor, T. R.·Loman, N. J.·The COVID-19 Genomics UK Consortium (COG-UK),

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Abstract

Genomic epidemiology has become an increasingly common tool for epidemic response. Recent technological advances have made it possible to sequence genomes rapidly enough to inform outbreak response, and cheaply enough to justify dense sampling of even large epidemics. With increased availability of sequencing it is possible for agile networks of sequencing facilities to collaborate on the sequencing and analysis of epidemic genomic data. In response to the ongoing SARS-CoV-2 pandemic in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed with the aim of rapidly sequencing 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 Majora, 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. The system was designed and implemented pragmatically to stand up capacity rapidly in a pandemic caused by a novel virus. This approach has underpinned the success of COG-UK, which has rapidly become the leading contributor of SARS-CoV-2 genomes to international databases and has generated over 60,000 sequences to date.

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Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Jackson, B., Rey, S., Amato, R., Livett, R., Goncalves, S., Harrison, E. M., Peacock, S. J., Aanensen, D. M., Rambaut, A., Connor, T. R., Loman, N. J., The COVID-19 Genomics UK Consortium (COG-UK),. 2020-10-07. MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. https://doi.org/10.1101/2020.10.06.328328

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