Microreact

Microreact (MR) is an online tool for viewing phylogenetic information, similar to Taxonium or Nextstrain Auspice. Like Terra, Microreact has a concept of workspaces (MR calls them projects) where you have an instance of the UI, with a specific URL, containing scientific information for some particular analysis.

For CalTBNet, we create one MR project per relevant cluster. This project contains:

• A nwk tree
• A backmasked nwk tree
• A distance matrix
• A backmasked distance matrix
• Links to the workspaces of parent/child clusters, if any
• Number of samples in the cluster
• Datestamp of when cluster first identified
• Datestamp of when cluster last updated

What's a relevant cluster?

At CDPH's request, all 10 and 5 SNP clusters are considered relevant clusters, but 20 SNP clusters are only considered relevant if they have a 10 SNP subcluster. A 20 SNP cluster that previously had no subclusters, but then gains one later, becomes relevant and will generate an MR project.

Known issues

• nwks where all samples are within 0 SNPs of each other do not render, resulting in "error loading component" where the tree should be
• Switching between panels or changing view options of a panel occasionally results in components not rendering correctly, requiring a refresh
• [likely an issue on my end, not MR's] On rare occasions, a new cluster made up entirely of old samples (remember, UShER is non-deterministic!) may fail to generate a new MR project
• [likely an issue on my end, not MR's] Parent-child cluster links are sometimes incorrect