A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Colquhoun, Rachel, O’Toole, Áine, Hill, Verity, McCrone, Jt, Yu, Xiaoyu, Nicholls, Samuel M, Poplawski, Radoslaw, Whalley, Thomas, Groves, Natalie, Ellaby, Nicholas, Loman, Nick, Connor, Tom ORCID: https://orcid.org/0000-0003-2394-6504 and Rambaut, Andrew 2024. A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK. Virus Evolution 10.1093/ve/veae083

PDF - Accepted Post-Print Version Available under License Creative Commons Attribution. Download (646kB)

Abstract

In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the United Kingdom. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme and to date this system has generated more than 3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision making, we developed a centralised pipeline that performs quality control, alignment and variant calling, and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.

Item Type:	Article
Date Type:	Published Online
Status:	In Press
Schools:	Biosciences
Additional Information:	License information from Publisher: LICENSE 1: URL: https://creativecommons.org/licenses/by/4.0/, Start Date: 2024-10-17
Publisher:	Oxford University Press
Date of First Compliant Deposit:	28 October 2024
Date of Acceptance:	14 October 2024
Last Modified:	28 Oct 2024 15:30
URI:	https://orca.cardiff.ac.uk/id/eprint/173469

Actions (repository staff only)

Edit Item