Trevor Bedford

This derives from the fact that we only specify `auspice_config_h1n1pdm.json` for both HA and NA and we don't have an epitope mask for NA epitope sites. To fix this we...

I believe this issue can be closed. Nextclade is launched and `/sars-cov-2` is a landing page. There is perhaps more work to be done, but I wouldn't tie it to...

>Is it a good idea to weight on population size? I was thinking per-country case counts over time might be better, but not sure where to get that data. Case...

Following from this, I worked from 1afb6d7e5278bad4a69801411d791d5b2cd7d5e8 and tried: ``` python3 scripts/get_population_sizes.py --output data/country_population_weights.tsv ``` from a freshly updated `nextstrain shell` command and got the following error ``` Traceback (most...

I really like where this is going! However, I ran into an error when trying to run this locally. In this filter step: ``` augur filter --metadata nextstrain-ncov-private/100k/metadata.tsv.xz --include defaults/include.txt...

Thanks for the feedback @victorlin. I have a couple thoughts: 1. In decent fraction of scenarios, I believe I'm going to want a "default" value for `population_weights.tsv`. As a simple...

I'm afraid I'm confused as to the push here. If you were to implement weighted subsampling in `augur` (per https://github.com/nextstrain/augur/issues/1318#issuecomment-2013653668), then we could take the existing YAML files like https://github.com/nextstrain/ncov/blob/master/nextstrain_profiles/nextstrain-gisaid/builds.yaml#L672...

Okay... maybe I'm catching up. The current YAML files generated by `nextstrain_profiles/nextstrain-gisaid/generate-subsampling-config.py` like `nextstrain_profiles/nextstrain-gisaid/subsampling/global_6m.yaml` are meant as just a refactor? And that these current YAML files would be replaced by...