Hi Duxx! I’m not a native English speaker myself, I totally understand
Thanks for your very helpful clarifications, now I understand much better and can give a proper answer.
I will rephrase your questions - let me know if my understanding is incorrect:
I want to visualise the results of a Nextclade CLI run in the Nexclade web app
This is currently not possible. There is a feature request on Github: ENH: Allow nextclade web to import pre-analyzed outputs · Issue #716 · nextstrain/nextclade · GitHub
There are two possible workarounds:
- (Simplest) Just use the web app to analyse your sequences
- (No internet required) Build and serve the web app locally, see nextclade/developer-guide.md at master · nextstrain/nextclade · GitHub
My question is: Why would you use a command like this and not just drop the Fasta on the website? Analysis is so fast now, the issue is more with RAM of the web app rather than running the alignment. Or do you have issues with browser compatibility? I would love to hear more from you on the reasons behind your request!
I want to allow others to view Nextclade results for a given set of sequences I control via a link
If we implemented a Nextclade JSON output viewer feature as requested above, this would be one simple side-effect.
However, given that the Nextclade JSON is much bigger than the input data (if zstd compressed) you can already do this in a way using Nextclade web’s URL parameters, see Nextclade Web — Nextclade documentation
For example, the following should direct the user straight to Nextclade web with a FASTA being auto downloaded and analyses: https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=https://data.clades.nextstrain.org/datasets/sars-cov-2/references/MN908947/versions/2022-01-05T19:54:31Z/files/sequences.fasta
So you in a way already use Nextclade community, by simply hosting your fasta somewhere on the internet, then crafting a URL that points at that fasta (see the docs). Just beware, you need to have CORS enabled - which isn’t by default on using Github (I think). So you may need to use a CORS proxy.
For example, I sometimes use regular Nextstrain builds are reference trees for fun in the following way:
I hope this helps - feel free to share more about your particular use cases - that’s what I can’t guess. You may have good use cases that we just haven’t thought about!