Cryptic transmission of SARS-CoV-2 in Washington State

Nextstrain build

WA clade analysis

Analysis of the predominant Washington State outbreak clade in Figure 2 of the manuscript can be produced by running snakemake from this directory. This will produce the file auspice/ncov.json, which can be visualized with Auspice. This file has been copied over to ncov-cryptic-transmission/auspice/ncov-cryptic-transmission_wa-clade.json. An interactive visualization of analysis results can be found at