Compare lineages with Pathoplexus WNV lineage calls. For data quality check and consistency, do a comparison against Pathoplexus samples and lineage calls (1A, 1B, 2, 3, 4, 5, 6, 7, 8, and "unassigned"). Determine if this is a reasonable global lineage system as compared to the USA based (pre-NY, NY99, WN02, SW03).
Potential Tasks
[x] Download Pathoplexus WNV lineage metadata
[x] Append Pathoplexus lineage columns to ingest metadata (estimated labor to this point ~2hrs)
[x] Build global phylogenetic tree, check that the lineages are reasonable
[x] Global pathoplexus WNV lineages calls are stable (estimated labor ~3hrs)
[ ] Within the global 1A lineage, inconsistent placement of USA-based strains (pre-NY, NY99, WN02, SW03)
[ ] Identify potential homoplasic mutations positions causing this issue
[ ] Attempt masking of problematic sites
[ ] Decide if we can create one global Nextclade dataset or if we need to separate by lineage similar to dengue
[ ] Perhaps compare nextclade results against WNV typer or check their true-negative (non-WNV) is unassigned in the Nextclade dataset
Context
Compare lineages with Pathoplexus WNV lineage calls. For data quality check and consistency, do a comparison against Pathoplexus samples and lineage calls (1A, 1B, 2, 3, 4, 5, 6, 7, 8, and "unassigned"). Determine if this is a reasonable global lineage system as compared to the USA based (pre-NY, NY99, WN02, SW03).
Potential Tasks
[x] Download Pathoplexus WNV lineage metadata
[x] Append Pathoplexus lineage columns to
ingestmetadata (estimated labor to this point ~2hrs)[x] Build global phylogenetic tree, check that the lineages are reasonable
[ ] Decide if we can create one
globalNextclade dataset or if we need to separate by lineage similar to dengue[ ] Perhaps compare nextclade results against WNV typer or check their true-negative (non-WNV) is unassigned in the Nextclade dataset