murallcl / ay25ay27

Builds and sequence lists for virological

AY25AY27 additional data

Builds and sample lists from comparison of Canadian AY.25 and AY.27 sequences to global for analysis in https://virological.org/t/monitoring-the-evolution-and-spread-of-delta-sublineages-ay-25-and-ay-27-in-canada/767.

Trees

The trees used to build the figures are:

• Figure 4: AY.25 tree (newick)
• Figure 5: AY.27 tree (newick)

These trees were built using Augur and the Augur build file is found at builds.yaml. Lists of the samples used are found in twentyfiveext and twentysevenext.

Figures

The figures for AY.25 and AY.25 are found in the following notebooks:

• Figure 4: AY.25 notebook
  • Other instructions
• Figure 5: AY.27 notebook
  • Other instructions

To run the analyses for Figures 4 and 5 you will need to install https://github.com/apetkau/genomics-data-index and Jupyter and also aquire the set of sequence data/metadata from GISAID (these are not provided).