Communities and functional potential
Shotgun metagenomics analysis
Explore which organisms and genes are represented in a microbial community. We scope read-based profiling, assembly and genome-resolved analysis around sequencing depth, community complexity and the questions your project needs to answer.
Who this service is for
For marine, soil, plant, environmental and host-associated microbiome researchers, biotechnology teams and laboratories. Projects can focus on community differences, metabolic potential, functional genes or reconstructed microbial genomes.
Discuss this analysisFrom inputs to interpretation
Analysis workflow
The final workflow is agreed after reviewing your data. Optional modules are selected for suitability and the research question.
Assess and prepare reads
Review quality, adapters, usable depth and sample consistency. Filter host or background sequences where appropriate and assess whether the remaining reads support the planned analyses.
Profile taxa and functions
Use suitable reference-based methods to characterise taxa and gene families. Build comparable sample tables and annotate selected pathways, explaining reference coverage and unclassified fractions.
Reconstruct genomes when justified
For suitable data, assemble reads, annotate contigs and recover metagenome-assembled genomes (MAGs). Evaluate completeness, contamination and abundance before interpreting genome-resolved functions.
Compare biological patterns
Relate taxonomic and functional patterns to the study design. Optional modules include CAZymes, biogeochemical pathways, AMR-associated genes and comparative MAG analysis.
Statistics and study design
Ordination, PERMANOVA with dispersion checks, differential abundance and environmental associations may be included. Methods are selected for the abundance data, replication and planned comparisons. Genome- and gene-level analyses consider shared ancestry, multiple testing and uneven detection where relevant.
Biological interpretation
Shotgun sequencing provides evidence of genetic potential. Gene detection does not establish transcription, enzyme activity, resistance phenotype or ecosystem process rates. An apparently absent pathway in a MAG may reflect incomplete genome recovery.
Outputs and deliverables
- QC summaries and annotated taxonomic, gene-family and pathway tables.
- Assemblies, gene catalogues and quality-assessed MAGs when these modules are included.
- Statistical comparisons, interpretation, figures and methods with relevant tool and database versions.
Scientific visualisations
Taxonomic profiles, pathway heatmaps, ordination, functional comparisons, genome-quality summaries and selected genome or gene-context figures. The figure set is selected to communicate the agreed comparisons and findings.
Scientific figure preparationDo you need MAGs, read-based profiling, or both?
Read-based profiling can answer many questions about differences among samples. MAGs add organism-linked genomic context, but recovery depends on coverage, community complexity and strain variation. We assess the value of assembly and binning for your dataset before including them in the scope.
Scope your project
Tell us about your dataset.
Tell us the sample count, approximate read depth, sample type, metadata and whether the priority is profiling, functional analysis, MAGs or a targeted gene set.
Send a brief description first. We agree data transfer, analysis scope, deliverables and a project-specific quotation before work begins.
BiomeLens provides bioinformatics and data analysis services. Laboratory sequencing, DNA/RNA extraction and wet-lab sample processing are not part of our services.