Cornelius Roemer

Right now we break up private mutations into: labeled, unlabeled and reversions. For monkeypox, I noticed that it would be nice to see sometimes if a mutation was simply already...

Brotli compresses datasets and wasm much better than gzip, it would be nice if we could take advantage of that. Using max compression comparison on SC2 tree and sample sequences,...

Inconsistency in how Ns are handled for genes vs nucleotide view

3

When I upload a partial genome, it is not evident in gene view that there are missing parts. It looks like the sequence is equal to reference in parts that...

UX: Run button should be higher up to make running more intuitive

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@emmahodcroft noticed earlier that the run button was quite far down when one added the example sequences - the run button moves as you add files. And I just noticed...

ENH: Avian flu datasets, e.g. H5

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I've received a request for Avian flu datasets e.g. H5, via Twitter DM. If you'd like this feature, feel free to leave a thumbs up here to signal support.

When a site is N, rather than showing it as N in auspice.json produced by Nextclade, we give it the base of the attachment point. This threw me off when...

The clade schematic needs updating, we're using a pre-BA.4/5 version. Here's the new one: https://github.com/nextstrain/ncov-clades-schema

PERF: Decompression using system zstd is quite a lot more efficient than using packaged zstd

1

Maybe not surprsingly, using standalone zstd for decompression and piping into nextclade is quite a bit faster than using the packaged zstd. I guess we could add some notes somewhere...

I read through the help for `--output-all` but I'm not quite sure it explains well what the argument is supposed to be. I _think_ it's the directory that we want...

ENH: More informative error when no value supplied to `--output-all`

1

When using `--output-all` but not passing any value, the error message is not as helpful as it could be. I would like to know what the possible values are, printing...