JT McCrone
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View article: A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK
A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK Open
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 sequenc…
View article: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK Open
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused l…
View article: Genomics-informed outbreak investigations of SARS-CoV-2 using civet
Genomics-informed outbreak investigations of SARS-CoV-2 using civet Open
The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local out…
View article: jtmccr1/figtreejs-react v0.0.1
jtmccr1/figtreejs-react v0.0.1 Open
Code as used in https://laduplessis.github.io/SARS-CoV-2_Guangdong_genomic_epidemiology/