Rachel Colquhoun, Áine O'Toole, Verity Hill, J T McCrone, Xiaoyu Yu, Samuel M Nicholls, Radoslaw Poplawski, Thomas Whalley, Natalie Groves, Nicholas Ellaby, Nick Loman, Tom Connor, Andrew Rambaut
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A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.
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 >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.
期刊介绍：
Virus Evolution is a new Open Access journal focusing on the long-term evolution of viruses, viruses as a model system for studying evolutionary processes, viral molecular epidemiology and environmental virology.
The aim of the journal is to provide a forum for original research papers, reviews, commentaries and a venue for in-depth discussion on the topics relevant to virus evolution.
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