eDNA & metabarcoding
Detect which taxa are present from environmental DNA—ASV inference, taxonomic assignment, and diversity, with primer and reference caveats stated.
Research Area
Marine Bioinformatics
The ocean is mostly unsequenced, and its organisms rarely have a tidy reference. We bring the computational depth to match: environmental DNA and metabarcoding for biodiversity, marine metagenomics, population genomics, and aquaculture genomic selection—for research, with the limits stated as plainly as the results.
Marine · often non-model
eDNA · metabarcoding · WGS
Biodiversity · popgen · aquaculture
Research predictions · no guarantees
Illustrative sample output
reef site
open water
sediment
Overview
Computational biology for the ocean, from a drop of seawater to a genome
A single litre of seawater carries DNA from hundreds of species; a marine genome is often large, repetitive, and unreferenced; and the questions—what lives here, how populations connect, how a stock adapts—are ecological and population-scale rather than single-sample. Marine data also brings its own gaps: reference databases are patchier for marine taxa, and eDNA signals are shaped by primers, shedding, and currents.
We work across that space: environmental DNA and metabarcoding for biodiversity, marine metagenomics for microbial communities, population genomics for connectivity and adaptation, and aquaculture genomics for breeding. The work runs through our core metagenomics, genomics, and pipeline services. Where we estimate breeding values or read eDNA, we are clear these are research findings and predictions: eDNA is a detection signal, not a census, and breeding values need validation in your population.
Applications
What we analyse in marine systems
The computational analyses that span a drop of seawater to a farmed genome—from biodiversity and community ecology to population connectivity and aquaculture breeding.
Biodiversity assessment
Alpha- and beta-diversity, rarefaction, and community comparison across sites, depths, and seasons.
Marine population genomics
Connectivity, structure, and adaptation across populations—robust even at the low coverage marine studies often have.
Aquaculture genomics
Genomic selection and breeding-value estimation for farmed species—framed as research predictions needing validation.
Coral & symbiont genomics
Host-symbiont (e.g. Symbiodiniaceae) analysis, disentangling holobiont partners in reef systems.
Marine microbial ecology
Community composition and function of marine microbiomes from metagenomic and amplicon data.
Environmental monitoring
eDNA-based screening for target, invasive, or indicator species over space and time—research, not certified testing.
Blue biotech & bioprospecting
Mining marine metagenomes for novel enzymes, biosynthetic gene clusters, and functions of interest.
The Pipeline
How a marine project runs
A transparent sequence from raw marine reads to an interpreted, reproducible result—methods and references chosen for the marker, organism, and question.
Steps adapt to your project: eDNA metabarcoding vs. metagenomics vs. population genomics vs. aquaculture selection. We agree the plan—and the caveats—with you first.
Scope & references
We agree the question and marker, and select reference databases—flagging where marine coverage is thin.
Inputs: reads · markers · plan
QC & preprocessing
Reads are quality-checked, trimmed, and denoised; primers removed for metabarcoding.
Tools: fastp · cutadapt · DADA2
Taxonomy or mapping
ASVs are assigned against SILVA/PR2/BOLD, or reads mapped and assembled for genomic work.
Tools: DADA2 · SILVA · BWA
Community or population analysis
Diversity and community structure, or population genomics—structure, connectivity, selection.
Tools: phyloseq · ANGSD · vegan
Domain analysis
Aquaculture selection, coral holobiont, or bioprospecting analyses as the project requires.
Tools: rrBLUP · antiSMASH
Interpretation & caveats
Results are interpreted with limits stated—eDNA detection vs. abundance, reference gaps, prediction uncertainty.
Focus: honest interpretation
Reporting & reproducibility
Figures, tables, and a written summary, with version-locked code and databases so it reproduces exactly.
Tools: Quarto · renv · conda
Tools & Technologies
Established, peer-reviewed tools—matched to your data
We select from the field's standard toolkit rather than forcing every dataset through one pipeline. A representative set of what we work with:
eDNA & metabarcoding
DADA2OBIToolsQIIME 2cutadapt
Metagenomics
Kraken2MetaPhlAnHUMAnNmetaSPAdes
Community ecology
phyloseqveganmicrobiome
Population genomics
ANGSDPLINKPCAngsdSTACKS
Aquaculture & selection
rrBLUPGBLUPAlphaSimR
Assembly & annotation
SPAdesFlyeantiSMASH
Phylogenetics
IQ-TREEMAFFTRAxML
Pipelines & environments
NextflowSnakemakecondarenv
Key Databases
The genomics resources we draw on
Cross-species analysis is powered by reference genomes, ortholog sets, and biodiversity databases. We build on the community's authoritative, versioned resources.
- SILVA
- Curated rRNA gene reference for bacteria, archaea, and eukaryotes.
- PR2
- Protist Ribosomal Reference — key for marine eukaryote metabarcoding.
- BOLD
- Barcode of Life Data System for species identification from barcodes.
- MarRef / MarDB
- Curated marine prokaryote reference and broader marine genome databases.
- OBIS
- Ocean Biodiversity Information System — global marine occurrence records.
- MGnify
- EBI metagenomics resource, including marine and Tara Oceans datasets.
- NCBI nt / RefSeq
- General sequence and reference collections for mapping and annotation.
- MetaZooGene
- Reference barcodes focused on marine zooplankton and metazoans.
- SILVA / MIDORI
- Marker references for metabarcoding across marine taxa and markers.
Choosing an Approach
eDNA metabarcoding vs. metagenomics vs. population genomics
Three marine approaches answer different questions. A quick orientation; we will help you match it to your study.
| Dimension | eDNA / metabarcoding | Metagenomics | Population genomics |
|---|---|---|---|
| Answers | Which taxa are present? | What can the community do? | How do populations differ? |
| Input | Marker amplicons | Shotgun reads | WGS or RAD-seq of individuals |
| Key limit | Reference gaps; not a census | Assembly & depth | Sample number & coverage |
| Best for | Biodiversity & monitoring | Function & novel genes | Connectivity, adaptation, breeding |
What You Receive
A complete, documented deliverable
Not just a taxa table dropped in a folder—a coherent picture of your samples, communities, or populations, documented so it reproduces.
- ASV/OTU table with taxonomy, or genotype matrix, as applicable
- Diversity & community-comparison results (eDNA/metagenomics)
- Population structure, connectivity & selection results, where applicable
- Estimated breeding values (GEBVs) with accuracy, for aquaculture work
- Functional/pathway or bioprospecting results, per your question
- Publication-quality figures (rarefaction, ordination, structure, trees)
- Reproducible methods with every tool & reference database version
Detection is not a census; a prediction is not a guarantee
Marine work carries two honest caveats we state up front. First, eDNA and metabarcoding measure detectability, not abundance or certainty of absence—results are shaped by primers, reference completeness, and how DNA disperses in water, so we report them as a biodiversity signal, not a headcount. Second, where we estimate aquaculture breeding values, these are statistical predictions with a stated accuracy that need validation in your population; field and production outcomes depend on environment and management, so we make no guarantees. We also flag where marine reference gaps limit what any method can resolve.
The practical payoff: you get results you can defend, with every tool and reference-database version recorded so the analysis reproduces exactly. And we will tell you plainly when sampling depth or reference coverage won't support the conclusion you're after.
FAQ
Marine bioinformatics questions
What marine, ecology, and aquaculture teams most often ask before starting.
Environmental DNA and metabarcoding reads, marine metagenomes, whole-genome and reduced-representation sequencing from marine organisms, and aquaculture genotyping data. Work starts once you have sequence data — from your core facility or a public repository.
No, and we're careful to frame it correctly. eDNA and metabarcoding give a presence-and-relative-signal picture of which taxa are detectable in a sample, shaped by primers, reference completeness, and shedding rates. It is a powerful biodiversity-screening tool, not an absolute census or abundance count.
Yes, for research. We estimate genomic breeding values and run selection analyses for aquaculture species. As with any breeding-value prediction, these are statistical estimates that need validation in your population and environment — we don't guarantee field or production outcomes.
It depends on the marker and question: SILVA and PR2 for rRNA, BOLD for barcoding markers, and marine-specific resources like MarRef/MarDB and OBIS. We're explicit that reference gaps for marine taxa can limit what any method resolves.
No. This is computational research support for marine biology, ecology, and aquaculture. We are not an accredited environmental or regulatory testing laboratory, and results should be treated as research findings rather than certified monitoring.
Marine projects are delivered through our core services — chiefly Metagenomics & Microbiome for eDNA and community work, Genomics & Variant Analysis for population and organismal genomics, and Custom Pipelines for scalable, reproducible workflows.
Related
The services that run this work
Have marine data waiting to be read?
Send us your eDNA reads, metagenomes, or marine genotypes—we'll scope the analysis and tell you honestly what it can and can't show.