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Fig. 10 | Genome Biology

Fig. 10

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

Fig. 10

Example Civet report based on a simulated outbreak. The customisable preamble can contain information such as a description of the outbreak, number of sequences of interest and authors of the report (A). The report also includes summary tables of the input data, split by whether the queries are in the COG-UK dataset or have been provided by the user (B). Civet displays summarised subtrees of the local phylogenetic diversity surrounding sequences of interest, with tips coloured by administrative level one region by default (C). Optionally, a timeline of the sequences can be displayed (D), and a ‘Snipit graph’ which highlights nucleotide changes from a defined reference genome sequence amongst the sequences of interest (E). Descriptive maps show the geographic distribution and the genetic diversity of SARS-CoV-2 circulating in the local area (F)

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