Genomics & transcriptomics
Microbiome & Microbial Genomics
We analyse microbial community data, from 16S or ITS amplicons and shotgun metagenomes, and sequence data from bacterial isolates, using statistics that respect the compositional nature of microbiome counts.
Who it is for
- Clinical, agricultural and environmental microbiome studies
- Microbiology labs sequencing bacterial isolates
- Groups comparing communities across treatments or sites
What you send us
- Amplicon FASTQ16S rRNA or ITS, demultiplexed or with barcodes.
- Shotgun metagenome FASTQShort-read community sequencing.
- Isolate FASTQIllumina and/or long-read data for genome assembly.
- MetadataGroups, sites, time points, and blanks or mock communities.
What you receive
- ASV or taxonomic profile tables
- Diversity and ordination figures
- Differential-abundance results with effect sizes
- Annotated genome assemblies and AMR gene reports for isolates
- Methods section and reproducible code
Methodology
How the work runs
Each step is agreed with you and documented. Typical tools: QIIME 2 · DADA2 · phyloseq · vegan · Kraken2 · MetaPhlAn · SPAdes · Bakta · CheckM2 · AMRFinderPlus
- ScopingStudy design, controls, primers or sequencing approach, and the comparisons you need.
- ProcessingDADA2 denoising to amplicon sequence variants, or read-based profiling with Kraken2 and MetaPhlAn; assembly and annotation for isolates.
- Taxonomy and diversityTaxonomic assignment, alpha and beta diversity, rarefaction and ordination.
- StatisticsPERMANOVA with dispersion checks and compositional differential-abundance analysis.
- ReportFigures, tables, interpretation and a methods section ready for a manuscript.
Quality controls
Checks applied to every project
- Negative controls and mock communities used to assess contamination
- Read retention through every processing step reported
- Rarefaction curves to show whether depth captured diversity
- Assembly completeness and contamination for isolate genomes
Scope and limits
What the work can and cannot show
- Amplicon data rarely resolve species reliably; taxonomy is reported at the rank the data support.
- Presence of an AMR gene does not establish phenotypic resistance.
- Research use only: results are not a clinical or diagnostic report.
Free quote
Start a Microbiome project.
Describe your data and questions. We reply with questions or a written quote.
It depends on the data type, the number of samples and the depth of interpretation you need. Every project receives a written quote with scope, deliverables, price and delivery date after a short exchange about your data and questions. The quote is free and carries no obligation.
Strongly recommended, especially for low-biomass samples. Without blanks it is difficult to distinguish contamination from real community members, and we will note this limitation in the report.
Data are used only for your project, transferred through a channel you approve and deleted at the end of the engagement on request. We will sign your institution’s confidentiality agreement before any data are shared.
Yes. You receive a methods section with software versions and parameters, and every figure can be regenerated from the delivered code. Authorship or acknowledgement follows your field’s norms and is agreed at the start.
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