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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

Samuel M NichollsRadoslaw PoplawskiMatthew J BullAnthony UnderwoodMichael ChapmanKhalil Abu-DahabBen TaylorRachel M ColquhounWill P M RoweBen JacksonVerity HillÁine O'TooleSara ReyJoel SouthgateRoberto AmatoRich LivettSónia GonçalvesEwan M HarrisonSharon J PeacockDavid M AanensenAndrew RambautThomas Richard ConnorNicholas J Lomannull null
Published in: Genome biology (2021)
In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence 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 CLIMB-COVID, 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.
Keyphrases
  • genome wide
  • sars cov
  • public health
  • respiratory syndrome coronavirus
  • single cell
  • coronavirus disease
  • cross sectional
  • machine learning
  • electronic health record
  • quality improvement
  • big data
  • deep learning