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Core and accessory gene repertoires

Microbial pangenome analysis

Characterise genes shared across a microbial genome collection and those that vary between strains. We design pangenome analyses around taxonomic scope, genome quality and sampling so that gene-content patterns remain biologically interpretable.

Who this service is for

For researchers and biotechnology teams investigating strain diversity, conserved functions, accessory repertoires or genomic traits. Isolate genomes are common inputs; MAGs require additional attention to missing and fragmented sequence.

Discuss this analysis

From inputs to interpretation

Analysis workflow

The final workflow is agreed after reviewing your data. Optional modules are selected for suitability and the research question.

  1. Review genome inclusion

    Check taxonomic consistency, quality and duplicate or near-duplicate sampling. Identify whether fragmented or incomplete assemblies could distort estimates of shared and variable genes.

  2. Build consistent gene families

    Harmonise annotation and select an appropriate ortholog-clustering strategy. Review parameters, paralogs and problematic gene calls rather than treating every inferred cluster as a reliable biological family.

  3. Characterise the repertoire

    Generate presence–absence tables and define core, accessory and rare categories using explicit thresholds. Examine functions, core-gene relationships and pangenome accumulation patterns where appropriate.

  4. Evaluate variation between groups

    Investigate agreed gene-content or functional differences while considering relatedness, sampling and missingness. Optional trait associations require an adequate design and suitable phenotype information.

Statistics and study design

Summaries may include gene-family prevalence, repertoire size, functional comparisons and resampling-based accumulation curves. Interpretation depends on genome number, quality and diversity. Trait associations need appropriate consideration of population structure and multiple testing.

Biological interpretation

Core-gene definitions depend on thresholds and the genome collection. Fragmentation, contamination and inconsistent annotation can create false absences or extra families. An apparent open or closed pangenome is conditional on sampling and analysis; gene-content associations do not establish adaptation or causality.

Outputs and deliverables

  • Genome QC/inclusion records, annotation summaries and gene-family/ortholog tables.
  • Core/accessory classifications with explicit thresholds and genome-by-family presence–absence matrices.
  • Scoped phylogenetic, functional or trait-comparison outputs, figures and documented interpretation of limitations.

Scientific visualisations

Gene presence–absence heatmaps, core/accessory summaries, annotated core-genome trees and accumulation curves when suitable. Labels, scales and genome metadata make comparisons traceable to the underlying tables.

Scientific figure preparation

Can incomplete MAGs be included?

They can be considered when quality and the scientific question justify it, but missing sequence makes gene absence harder to interpret. We discuss quality thresholds, taxonomic breadth and sensitivity analyses before combining MAGs with isolates. Missing annotations should not automatically be treated as true biological absences.

Scope your project

Tell us about your dataset.

Include genome count, taxonomic scope, assembly and annotation availability, quality information and the group or trait comparison you want to investigate.

Send a brief description first. We agree data transfer, analysis scope, deliverables and a project-specific quotation before work begins.

Start a project enquiry

BiomeLens provides bioinformatics and data analysis services. Laboratory sequencing, DNA/RNA extraction and wet-lab sample processing are not part of our services.