About
A platform built around biological questions.
QuestOmics is a human gut microbiome analysis platform. We focused it on the questions researchers actually ask, not on the pipelines that answer them.
Why we built it
Microbiome research moves slowly when most of the work is plumbing. Stitching together tools, formats, and clusters eats the time that should go into asking biological questions. QuestOmics removes that friction: you describe what you want to learn, and the platform runs the right, reproducible analyses for you.
Question-driven analysis
Instead of picking a pipeline and figuring out what it can tell you, you pick a question. “What organisms dominate this community?”, “Are AMR genes present?”, “How does this cohort compare to published studies?” QuestOmics then activates the curated, compatible analyses for it. Incompatible options stay disabled. No manual tool selection. No glue code.
What you can analyze
QuestOmics is built for human gut microbiome data. Supported inputs include shotgun metagenomes (short and long reads), 16S rRNA amplicons, bacterial isolates, and pre-assembled contigs or MAGs.
- Taxonomic profiling: 16S and shotgun metagenomic composition.
- AMR / resistome screening: detection of resistance genes across the community.
- Functional pathway profiling: which metabolic pathways are active across your samples.
- Differential abundance: which species differ between groups, adjusting for covariates.
- Cohort comparison: placing your samples next to thousands of published gut metagenomes.
- Diversity: within and between samples; the standard ecology metrics, plotted.
Interpretation grounded in literature
Tables are not interpretation. Every analysis is paired with Gut Assistant, an AI layer built specifically for microbiome science. It reads from a curated library of peer-reviewed papers and only cites what’s really there. Not hallucinations.
Reproducible by design
Every run is sealed and version-pinned, so anyone can reproduce it. Software versions are recorded at execution time. Methods text is auto-generated per run, ready to paste straight into a Materials & Methods section. Reports come out structured for manuscript use, with figures, tables, and citations included.
Our commitments
Your sequencing data and analysis results belong to you and your study. They are never used for external research, never pooled into external datasets, never sold, and never used to train external models. Data is stored on private, secure hardware in the EU.
Who’s behind it
Sandro Valenzuela
BSc in Bioinformatics · PhD in Infant Gut Microbiome
QuestOmics is a one-person labor of love right now, built by a microbiome scientist who got tired of the plumbing getting in the way of the questions. If that resonates, I’d love for you to take it for a spin: open a workspace, upload a dataset, and ask your first question. And once you’re inside, reach out through Gut Assistant. I read every message and I’d genuinely like to hear what you’re working on.
Prefer email? I’d love to hear from you, so write to me anytime at sandro.valenzuela@helsinki.fi.
Get started
Create a workspace, upload a dataset, and ask your first biological question.