TY - JOUR
AU - Colquhoun, Rachel M.
AU - O’Toole, Áine
AU - Hill, Verity
AU - Yu, Xiaoyu
AU - Poplawski, Radoslaw
AU - Whalley, Thomas
AU - Groves, Natalie
AU - Ellaby, Nicholas
AU - Loman, Nick
AU - Connor, Tom
AU - Rambaut, Andrew
AU - McCrone, John T.
AU - Nicholls, Samuel M.
PY - 2024
DA - October
TI - A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK
JO - Virus Evolution
VL - 10
IS - 1
DO - https://doi.org/10.1093/ve/veae083
AB - 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 UK. 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 &gt;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 centralized 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.
PB - Oxford University Press
UR - https://www.research.ed.ac.uk/en/publications/012f7db2-a4dd-427c-a543-0bef11175130
KW - Coronavirus (COVID-19)
ER