New in Solu: Cluster analysis

Do not index

Our latest release introduces a brand new view for cluster analysis - designed to help you draw more confident conclusions about the relationships between samples.

New cluster view

When Solu platform detects a cluster, it will automatically generate a view and a name for it (visible on the sidebar on the left).

Any two samples that have less than 20 SNP distance (high quality SNPs) will be considered a cluster. Note that the distances between individual samples can be larger than this threshold, particularly in clusters that have many samples or samples that have evolved over a long time.

Cluster context

The context section helps you gauge how far the cluster is from the nearest outgroup samples.

By dragging the SNP slider, you can prune the phylogeny to filter out samples that are a certain SNP distance away - essentially zooming in and out in the tree.

This is particularly helpful in cases where the distances are so large that a regular phylogenetic tree would be unreadable.

Reconstructed transmission trees (beta)

We are also able to compute a reconstructed transmission tree based on the sampling dates and evolutionary differences.

Transmission pathways are estimated by doing an ancestral reconstruction of a dated phylogeny. The transmission chain is inferred by identifying the most likely transmission events between individuals based on the phylogenetic tree and the sampling dates.

We are running manual checks to ensure this feature operates smoothly, which is why it's currently available on an opt-in basis. Please let us know if you're interested in analyzing transmission dynamics within your cluster!