Replaces the current table of derived haplotype frequencies and titer references that is based on a subsampled HA tree with a table based on all available sequences during the same time period.
With the latest version of Nextclade, we can determine derived haplotype strings per record from a Nextclade annotations file with columns for clade and mutations relative to each clade. We can then calculate haplotype frequencies from all available data instead of a subset of data used to build a tree.
Development checklist
[x] Identify derived HA1 haplotypes from all data with Nextclade for haplotypes
[x] Estimate frequencies per haplotype from all data including at 4 weeks ago and 8 weeks ago, reporting delta frequency for that time period
[x] Include distinct references per haplotype across all titer collections (e.g., cell FRA, cell HI, egg FRA, egg HI, etc.)
[x] Generate table of haplotype frequencies and references with links to haplotype view in the corresponding tree
Description of proposed changes
Replaces the current table of derived haplotype frequencies and titer references that is based on a subsampled HA tree with a table based on all available sequences during the same time period.
With the latest version of Nextclade, we can determine derived haplotype strings per record from a Nextclade annotations file with columns for clade and mutations relative to each clade. We can then calculate haplotype frequencies from all available data instead of a subset of data used to build a tree.
Development checklist
Related issue(s)
Related to #130 Depends on https://github.com/nextstrain/nextclade/pull/1492
Checklist