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loculus-project / loculus

An open-source software package to power microbial genomic databases
https://loculus.org
GNU Affero General Public License v3.0
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Client-side consensus calling using ViralWasm-Consensus? #2637

Open niemasd opened 2 weeks ago

niemasd commented 2 weeks ago

First of all, amazing work! I've been hoping for something like this for quite some time!

It seems like users upload consensus sequences, which is standard at the moment, but is there any interest in adding support for client-side consensus sequence calling from raw or mapped reads using ViralWasm-Consensus?

ViralWasm-Consensus uses biowasm to run WebAssembly-compiled versions of tools like fastp, Minimap2, and ViralConsensus client-side in the user's web browser without any need for manual installation of any tools

I can imagine having an upload interface where, if the user picks a FASTQ file, it automatically gets mapped to the viral reference genome and gets a consensus sequence called directly within their own browser, without any manual action on their part

The rationale for such functionality is to prevent/minimize bioinformatics errors from users (e.g. those seen in the early days of the COVID-19 pandemic)

chaoran-chen commented 2 weeks ago

Hi Niema, you're the first one to create an issue since our release - welcome and thank you! This is a very interesting suggestion. We have the plan to support the upload and server-side processing of raw sequences at some point but a client-side assembly is also a very interesting idea. It's at the moment not at the top of our priority list (we first want to focus on improving the experience with only consensus sequences) but will be happy to consider your suggestion when we start working on the support of raw sequences.

niemasd commented 2 weeks ago

Sounds good! Feel free to ping me if/when the interest ever arises! I'm going to tag @robertaboukhalil (the developer of biowasm) so that he's in the loop if that ever happens, as I think this would be an amazing use-case for biowasm (it's something he and I have chatted about in the past)

robertaboukhalil commented 2 weeks ago

Yes, count me in!

theosanderson commented 2 weeks ago

Thank you Niema for the issue and Robert for the enthusiasm! As Chaoran says we probably don't have resources to take this on atm this second, but it is something I think would be a really nice feature for the world to have as part of the bioinformatics ecosystem in the future. One can imagine it as a core feature of a database, but also potentially as an external tool that uses the database's submission API.