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 https://nextstrain.org/community/blab/ncov-cryptic-transmission/introductions.