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A multichannel pipette draws liquid from a reagent reservoir beside a 96-well microplate.

Photo: James Gathany / CDC (PHIL #23206). Illustrative of laboratory practice — not a VAMS facility or team.

For laboratories

Add structured microbiome intelligence to compatible sequencing workflows.

VAMS ATLAS™ can provide a structured reporting and interpretation layer over microbiome data workflows it is compatible with — assessed against method, quality and metadata rather than assumed.

Discuss laboratory collaboration Explore ATLAS reporting View sample report

Inputs and where they stand

Compatibility is a case-by-case assessment. The labels below describe how often a workflow of that type proves compatible — not a guarantee for any specific one.

Raw FASTQ

Paired or single-end reads with run metadata. The most common starting point.

Commonly supported

Processed tables

Feature or taxonomy tables where the upstream method is documented and reproducible.

Assessed case by case

16S amplicon

Marker-gene composition and diversity. Region and primer set need to be declared.

Commonly supported

Shotgun metagenomics

Species-level structure and functional potential, coverage permitting.

Commonly supported

Metatranscriptomics

Expression context at the sampled timepoint.

Limited — discuss first

ITS / fungal

Mycobiome context where the assay supports it.

Limited — discuss first

From accepted input to structured output

One analysis path for every compatible workflow: QC and method-fit checks gate entry, analysis runs on a recorded pipeline version, and the output states its method support.

  1. Accepted input Raw reads or already-processed tables, with the method and run details that produced them. FASTQ readsProcessed tables
  2. 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.
  3. Analysis Taxonomic or functional assignment, run on a recorded pipeline version.
  4. Structured output Tables and figures returned with the method, pipeline version and the limits that apply to them.
Illustrative overview of the analysis path for externally generated sequencing data. Accepted formats and checks depend on the method and the study design agreed in advance.

Three methods, three different questions

Method choice is part of the compatibility assessment. Each method answers a different question from the same sample, and none supersedes another.

One sample · three different questions

16S Foundation™

Question it answers

What is present, and how is the community structured?

Reads out

  • Marker-gene composition
  • Diversity measures
  • Ecological context

Cannot resolve

  • Species-level identity within closely related groups, such as Lactobacillus
  • Functional genes, which sit outside the marker region

WGS Advanced™

Question it answers

Which species are present, and what could the community do?

Reads out

  • Species-level structure
  • Gene content across genomes
  • Functional potential

Cannot resolve

  • Whether any annotated gene is actually being expressed
  • Organisms falling below the depth reached in a run

MetaT Functional™

Question it answers

What was being expressed when the sample was taken?

Reads out

  • Expression context at the sampled timepoint

Cannot resolve

  • Conditions before or after that timepoint
  • Genes present but not being transcribed at that moment

Not a ladder — no method supersedes another.

The three methods answer different questions and are not ranked against one another. Each has boundaries; the appropriate method depends on the question being asked. Order of presentation carries no meaning.

What the interpretation layer needs

ATLAS states the method support behind every output, which means the method has to be known. These are the inputs that make that possible.

  • Declared amplicon region and primer set, where applicable
  • Run-level QC metrics and negative controls for low-biomass specimens
  • Stable sample identifiers and chain-of-custody metadata
  • Consistent library preparation within a batch
  • Documented, reproducible upstream processing for processed inputs

Where a workflow is a poor fit

Undocumented upstream processing, missing controls on low-biomass specimens, or a method that cannot resolve what a score claims to measure. In those cases the honest answer is that the interpretation layer should not run — and we will say so.

Where ATLAS sits in your pipeline

  1. Your sequencing Platform and method you already run
  2. Accepted input Raw FASTQ or documented processed tables
  3. QC & method fit Declared region, controls, metadata
  4. ATLAS™ processing Governed interpretation
  5. Structured output Scores, panels and packs with confidence
  6. Your reporting Human-readable and machine-readable
Compatibility is assessed against method, region, depth and metadata rather than platform alone — these stages describe the shape of the workflow, not a guarantee for any specific one.

Ways a collaboration can be scoped

  1. ATLAS reporting over your sequencing

    You sequence; ATLAS provides the structured interpretation and reporting layer.

  2. Sequencing collaboration

    Your facility performs sequencing for VAMS-originated samples under agreed methods.

  3. Referral

    You refer microbiome work to VAMS where it falls outside your current scope.

  4. Technology or integration collaboration

    Deeper workflow or data integration, scoped against what is genuinely supported.

Technical questions

Is ATLAS compatible with our platform?

Compatibility depends on method, region, depth and metadata rather than platform alone, so it is assessed case by case. We would rather tell you a workflow is a poor fit than accept data the interpretation cannot support.

Do you offer an API?

Integration is discussed against what is genuinely supported at the time. We do not advertise integration surfaces that are not in production.

What volume do you work with?

Tell us your approximate volume and we will say honestly whether it fits.

Is accreditation required?

Not to begin a conversation. It is optional on the enquiry form and matters more for some collaboration models than others.

Discuss laboratory collaboration

Tell us about your workflow

Platform, methods and approximate volume are enough for a first conversation. Accreditation is optional.

  1. 1About you
  2. 2Your laboratory
  3. 3Capability
  4. 4Context
About you