Cryptic transmission of SARS-CoV-2 in Washington State

Nextstrain build

Introduction analysis

Analysis of introductions to Washington State in Figure 1 of the manuscript can be produced by running snakemake -s Snakefile_Regions from this directory. This will produce the file auspice/ncov_washington.json, which can be visualized with Auspice. This file has been copied over to ncov-cryptic-transmission/auspice/ncov-cryptic-transmission_introductions.json. An interactive visualization of analysis results can be found at