Adds rules and scripts to the early SC2 workflow to sample ~2000 sequences from Nextstrain clade 21J (Delta), find clusters from a t-SNE embedding of these sequences, and compare these clusters to collapsed Pango lineages. Adds a new paragraph to the end of the main SARS-CoV-2 section of the manuscript, adds a supplemental figure of counts per lineage/cluster, and adds a row to the supplemental accuracy table with the accuracy of the clusters from this analysis.
Description
Adds rules and scripts to the early SC2 workflow to sample ~2000 sequences from Nextstrain clade 21J (Delta), find clusters from a t-SNE embedding of these sequences, and compare these clusters to collapsed Pango lineages. Adds a new paragraph to the end of the main SARS-CoV-2 section of the manuscript, adds a supplemental figure of counts per lineage/cluster, and adds a row to the supplemental accuracy table with the accuracy of the clusters from this analysis.
Related issues
Closes #110