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