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Microbial isolate genomes

Microbial whole-genome analysis

Turn microbial isolate sequencing reads into a quality-assessed genome and a clear account of its identity and functional repertoire. BiomeLens provides the bioinformatics analysis of WGS data, with additional comparisons selected for your research aims.

Who this service is for

For culture collections, microbiology laboratories, environmental researchers and biotechnology teams characterising bacterial or archaeal isolates. We support single-isolate and multiple-strain projects, including review of existing assemblies and annotations.

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. Confirm data suitability

    Review read quality, coverage and evidence of mixed or unexpected sequence content. Check isolate-to-file mapping and clarify material quality issues before downstream interpretation.

  2. Assemble and evaluate

    Choose a suitable short-read, long-read or hybrid strategy. Assess assembly size, fragmentation and relevant completeness/contamination evidence. Report circular or complete assemblies only when supported.

  3. Resolve identity and annotate

    Assess taxonomic placement using genome-level evidence and suitable references, including average nucleotide identity (ANI) where relevant. Annotate genes and functions with traceable database versions.

  4. Investigate functions and context

    Examine pathways, candidate enzymes or other agreed traits. Comparative genomes, plasmid context and AMR- or virulence-associated gene screening can be added where supported.

Statistics and study design

A single isolate primarily supports descriptive genome characterisation. Multiple-isolate comparisons can include genome similarity, phylogenomics and gene-content differences. Group-level inference requires an appropriate sampling design; genes and contigs are not independent biological replicates.

Biological interpretation

Genome assignments can differ from marker-gene identifications because of reference coverage, nomenclature, resolution or sample-quality issues. We compare the evidence and document unresolved conflicts. Gene detection alone does not establish a resistance phenotype, pathogenicity or experimental activity.

Outputs and deliverables

  • Read and assembly QC summaries, agreed assembly files and documented quality limitations.
  • Gene annotations, selected functional tables, taxonomy and genome-similarity evidence.
  • Genome figures, methods and an interpretation discussion; comparative outputs when included in the scope.

Scientific visualisations

Assembly-quality summaries, genome or gene-context maps, ANI heatmaps and phylogenetic trees where suitable comparison genomes exist. Plasmid and pathway figures distinguish supported findings from computational candidates.

Scientific figure preparation

What if WGS and an earlier 16S identification disagree?

We review read/assembly quality, sample identities, reference genomes, taxonomic frameworks and comparison coverage. Any conflicting assignments are evaluated against the supporting evidence. Some discrepancies require clarification with the laboratory or sequencing provider.

Scope your project

Tell us about your dataset.

Include the isolate count, platform, read types, available assemblies, prior identification evidence and the traits or pathways you want investigated.

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.