Cluster Investigation and Virus Epidemiology Tool

civet was developed to aid SARS-CoV-2 outbreak investigations and enable robust analysis to be performed and reports generated as rapidly as the data was being produced.

civet puts new sequences into the context of known background diversity, and can summarise the background diversity based on the users input.

How to cite

O'Toole et al 2021. medRxiv preprint

Civet Documentation

Quick start walkthrough

Example reports

Installation and updating

Background data set & setting up your first civet run

Running civet

Run options and configuration