Ivan Aksamentov

Some additional thoughts from the internal discussion: The idea is to take the first sequence in the input fasta file and run the seed matching part of the alignment algorithm...

@trvrb noted that this: > the first sequence in fasta happens to be low quality can be mitigated by taking ~10 sequences at random from the FASTA (instead of just...

A couple of UX challenges involved: How does the workflow will look like for the user compared to what we have now? Do we mandate autodetection? What if user just...

Hi @xzhub, No, there isn't. We haven't thought about it. Should not be hard, because Nextclade is just a static React web app. There is no API server, and the...

Nextclade algorithm was recently rewritten in C++, and web version uses it in the form of a WebAssembly (wasm) module, so you need to build wasm first, and then the...

@corneliusroemer Might be nice to have. It is important to not mess up the caching. And data and code updates should be handled well. Contributions welcome.

> at the expense of higher memory Conflicts with https://github.com/nextstrain/nextclade/issues/446, https://github.com/nextstrain/nextclade/pull/451 Close old Nextclade tabs, it might make things more snappy. Current overscan is 10 rows https://github.com/nextstrain/nextclade/blob/a2fc19b13b89a4b905e9a37e6b3724119cb1758e/packages/web/src/components/Results/ResultsTable.tsx#L556 How many you'd...

SVG rendering is slow, synchronous and single-threaded in the current browsers. And it becomes slower for us as more and more markers need to be rendered. I could not possibly...

@fanninpm You can always do the compression yourself if you'd like: ``` nextclade --output-fasta=- | xz -2 > {output.alignment} ``` How would you imagine a flag would look like? What...

> I imagine that for every --output-* flag, there could be a corresponding --compressionlevel-* flag. That would be a lot of flags! @corneliusroemer @rneher What do you think? @fanninpm Before...