Genomics-informed outbreak investigations of SARS-CoV-2 using civet.

ABSTRACT: The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the quer

SUBMITTER: O'Toole A 

PROVIDER: S-EPMC10021969 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature