From sample collection to scientific interpretation
A transparent, end-to-end account of how a swab or stool sample becomes sequencing-derived microbial context — with quality control, reference cohorts, and confidence indicators documented at each step.
We publish our methodology so that results can be judged on their process, not just their presentation. This page walks through collection, laboratory processing, extraction, sequencing, quality control, and the interpretation framework that turns validated data into readable context. Outputs describe associations, not causation, and are never intended to diagnose, treat, or cure.
Scientific Principles
Restraint, traceability, and honest uncertainty guide every decision from bench to report.
Three principles hold the methodology together. First, traceability: each insight can be followed back to the sequencing signal and reference cohort it came from. Second, calibrated confidence: results carry indicators that show how strongly a pattern can be read, so nothing is overstated. Third, bounded scope: we report sequencing-derived microbial context and clearly mark where interpretation ends. These principles keep the science useful for curious readers and defensible for healthcare professionals reviewing the same data.
Sample Collection
Sample Collection explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
Sample Collection presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
Laboratory Processing
Laboratory Processing explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
Laboratory Processing presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
Derived from sequencing data. For educational and informational use only; not intended for diagnosis or treatment.
DNA & RNA Extraction
DNA & RNA Extraction explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
DNA & RNA Extraction presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
Sequencing Technologies
Sequencing Technologies explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
Sequencing Technologies presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
Derived from sequencing data. For educational and informational use only; not intended for diagnosis or treatment.
Quality Control
Quality Control explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
Quality Control presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
Interpretation Framework
Interpretation Framework explains the scientific role this topic plays within VAMS BIOME’s microbiome intelligence architecture.
Interpretation Framework presents the scientific workflow behind VAMS BIOME, from collection and laboratory processing through sequencing, quality control, computational analysis, and reporting.
See the methodology behind every ATLAS™ read
Trace any result back to the sample, the sequencing method, and the reference cohort that shaped it — with confidence indicators visible throughout.
- ✓ Standardized collection
- ✓ Molecular extraction
- ✓ Sequencing preparation
- ✓ Quality control
- ✓ ATLAS interpretation
Derived from sequencing data. For educational and informational use only; not intended for diagnosis or treatment.
At the bench
Methodology is bench discipline before it is data.
Every downstream number depends on unglamorous physical care — controlled environments, clean transfers, documented steps. The frameworks on this page describe that discipline; they never substitute for it.
Methodology, illustrated
The path a sample takes — and the path data takes.
Two rails carry every result: the laboratory path from collected sample to sequence, and the analysis path that checks, processes and structures the data before interpretation.
- 01 Collection Sample collected following the kit instructions and returned for processing.
- 02 Extraction Nucleic acid recovered from the sample material.
- 03 Library preparation Fragments prepared and indexed so each sample stays traceable.
- 04 Sequencing Prepared libraries are read on the sequencer.
- 05 Bioinformatics Reads pass quality control, then taxonomic or functional assignment.
- 06 Structured output Tables and figures, versioned with the method and pipeline used.
- Accepted input Raw reads or already-processed tables, with the method and run details that produced them. FASTQ readsProcessed tables
- QC and method fit Read quality, depth, completeness and metadata are checked, and the data is tested against what the method can support. Does not pass: held and returned with the QC reasons, rather than analysed with a caveat.
- Analysis Taxonomic or functional assignment, run on a recorded pipeline version.
- Structured output Tables and figures returned with the method, pipeline version and the limits that apply to them.