How it works
From sequencing files to a manuscript-ready report.
You tell QuestOmics what you want to learn. It picks the right tools, runs them, and writes up the result. Here’s the full path a project takes, step by step.
At a glance
- Create a project and upload sequencing data.
- Describe your samples in the metadata table.
- Pick a biological question, and compatible analyses activate.
- Launch the run; containerized pipelines do the work.
- Read interpretable results with literature-grounded interpretation.
- Generate your manuscript, with figures, tables, and methods, and get your submission helper files.
Create a project and upload your data
Create a project and tag it with the cohort context (for example, “Adult IBD case-control” or “Infant gut development”). Drag FASTQ reads, assembled FASTA, or MAG files into the workspace. Uploads are duplicate-aware, so the same file isn’t ingested twice. The platform recognizes the input type automatically and routes it to the compatible analyses.
Drop FASTQ · FASTA · MAG files
or browse; duplicates skipped automatically
Describe your samples
Open the sample metadata table and fill in what each sample represents: sample ID, group, sequencing platform, study context. Differential abundance and cohort comparison need group labels (and a minimum of three samples per group, across at least two groups). Required columns are validated up front, before you spend any credits.
Group
case
Platform
Illumina
Group
control
Platform
Illumina
Group
-
Platform
-
Choose a biological question
Open the biological-question picker. You’re not choosing a pipeline; you’re choosing what you want to know: taxonomic composition, AMR carriage, functional pathways, differential abundance, cohort benchmark, or diversity. Compatible questions activate based on the data you uploaded; incompatible ones stay disabled with the reason shown.
Review and launch the run
Each analysis lists its ATP cost and a runtime estimate before you launch. Queued runs execute on sealed, versioned environments, so the same inputs always produce the same outputs. You can monitor live status from the dashboard and queue several questions in parallel.
Ready to launch
Compare two groups uses MaAsLin3
Read interpretable results
Outputs are organized by question, not by tool. Abundance tables, diversity metrics, and interactive charts open inline. Gut Assistant adds a plain-language interpretation grounded in the human gut microbiome literature, with citations to the source papers, not hallucinated references.
Gut Assistant
“Elevated Prevotella copriin the IBD group aligns with pro-inflammatory mucosal associations [1].”
Export a manuscript-ready report
Export a structured report: figures, tables, citation list, and an auto-generated methods section with pinned software versions. The methods text is written to drop straight into a Materials & Methods section, with no rewriting required.
Common patterns
A few of the workflows researchers run on QuestOmics:
Profile a single stool metagenome
Upload one FASTQ pair, pick “Taxonomic profiling” and “AMR screening,” and get a composition table, diversity metrics, and a resistome summary in one run.
Compare two groups
Label samples as case / control (or any two-group design) and run “Compare groups”, with statistical backup that adjusts for things like age, sex, or diet, then double-checked with a second method.
Benchmark against published cohorts
Run “Compare to public studies” to place your samples against thousands of published gut samples.
Write the methods section in one click
After your analyses complete, export the report, and the methods text, with pinned versions and references, comes with it.
Credits and capacity
Analyses run on ATP: pay-as-you-go credits that never expire. Storing samples uses Vacuoles: a monthly allowance, like a phone plan. Plans bundle both. The cost of each analysis is shown before you launch it, so there are no surprises.
ATP
pay-as-you-go · no expiry
Vacuoles
monthly allowance · renews each month
Start your first project
Open a workspace, upload a dataset, and ask your first biological question.