Forum:Idea: Cloud-based genome annotation & visualization tool — looking for feedback

Question

[GeneScope]

Hi everyone,

I’m exploring an idea for a web-based tool that simplifies genome annotation and visualization, and I’d love to get feedback from the community. Existing genome browsers (like IGV, UCSC, or JBrowse) are powerful, but they can be:

• difficult to install or configure,
• not truly cloud-based or collaborative,
• and sometimes hard to use for researchers who just want to upload and explore their own data quickly.

The concept is a SaaS platform where users could:

• upload sequences (FASTA, GFF3, VCF, etc.),
• automatically detect and annotate genes, exons, promoters, repeats, and SNPs,
• visualize these features interactively in the browser (like a “Google Maps for DNA”),
• and optionally integrate public data from Ensembl, NCBI, ClinVar, or gnomAD.

The goal is to make genome exploration more intuitive, especially for researchers or clinicians who don’t have a bioinformatics background but still need to interpret sequence data or variants.

I’d love to hear your thoughts:

• Which features would be most useful to you?
• What pain points do you currently face with genome browsers or annotation tools?
• Would a collaborative, browser-based interface fit into your workflow?

Any feedback, ideas, or critical perspectives would be greatly appreciated. If anyone’s interested in discussing this further or beta-testing at some point, please reach out!

Thanks

[Arup Ghosh]

These are some tools and platforms that offer similar functionalities.

• VarFish: https://www.varfish.de (data management, variant annotation, visualisation)
• 42basepairs: https://42basepairs.com/browse (WASM-based platform for genomic data visualisation)
• wANNOVAR: https://wannovar.wglab.org (variant annotation)
• GenomeSpy: https://genomespy.app (GPU-acclerated genomic data visualization framework)
• GeneBe: https://genebe.net/hub (Unified variant annotation database)

[GeneScope]

Thanks a lot for the thoughtful feedback and tool suggestions. I really appreciate it!

You’re absolutely right that there are already many strong solutions out there, and I don’t want to reinvent the wheel. My main interest is to explore whether there’s space for something that’s more user-friendly, accessible, and collaborative, especially for smaller labs, clinicians or students without deep bioinformatics experience.

I completely agree that adoption, cost, and usability are key challenges. At this stage I’m mostly trying to understand where current tools fall short and what would make people actually switch or try something new.

Thanks again for the insights, these are very helpful perspectives!

GeneScope

Answer 1

[GenoMax]

The concept is a SaaS platform

There are existing tools (e.g. HGMD Pro, DNANEXUS, GOLDENHELIX etc.) in the space that already use this model. Unless people have access to an institutional license these sort of tools remain out of reach of majority of users because of cost. That is where tools like IGV (which are free) show their utility.

The goal is to make genome exploration more intuitive, especially for researchers or clinicians who don’t have a bioinformatics background but still need to interpret sequence data or variants.

That goal is admirable but unless you find a magical way to make it super affordable, your tool will always be competing against open source/free software. It can also be tricky to design tools that would be used by people who don't have the proper background knowledge.

I’m exploring an idea for a web-based tool that simplifies genome annotation and visualization

Is this the first product you are contemplating or are there other offerings already available.

Are you at an institution which has an administrative unit in place to manage licensing/legal/compliance. Most of the developed countries have security/privacy laws for patient data, which in turn means formal business agreements will/may be required for using your software.

[Mensur Dlakic]

Agree with everything that's been said here, and a couple of other things to consider. Most people use the tools because of features, price or convenience. Usually a combination of all of three. Let's say that someone makes a free or more affordable tool with extra features. It still may not become popular because it needs to be advertised and reach the desired audience. It is difficult to get the users to learn something or change their habits unless there is a compelling reason.

It is difficult for me to imagine a scenario where a single person has the time or resources to make a tool that would be cheap or free, and on top of that has enough connections and business savvy to convince many people to use it. Assuming that all these things could happen, what would be the motivation to do it for little or no money? A pure altruism?

Answer 2

[Jeremy Leipzig]

First, check out the graveyard...

List of cloud genomics companies