Metagenomics bioinformatics services
Metagenomics Services for Shotgun and Amplicon Sequencing Projects
Downstream analysis of your metagenomic data: taxonomic profiling, functional annotation, diversity analysis and metagenome-assembled genome recovery, shaped around your research question.
We work with existing FASTQ files, pre-assembled contigs or processed tables from your sequencing core or provider. Sequencing and sample preparation are arranged separately.
Analysis capabilities
Our Metagenomics Services
Choose a complete analysis or selected steps. Shotgun sequencing and marker-gene amplicon data answer different questions; we agree the appropriate route and deliverables before starting.
Quality control & host filtering
Inspect sequencing quality, trim adapters and filter reads where appropriate. Tools may include FastQC, Trimmomatic and KneadData. Host-read filtering is agreed around the sample type and available reference data.
Amplicon-based microbiome analysis
For 16S, 18S or ITS marker-gene data, we provide denoising, ASV inference, taxonomic classification and diversity analysis using approaches such as DADA2 and QIIME2. See our microbiome data analysis services for this dedicated route.
Research outcomes
What can you achieve with our metagenomics services?
Describe community composition
Investigate which microbial groups are detected and how their relative representation varies between samples. Interpret differences in the context of the sampling and sequencing methods.
Explore functional potential
Identify candidate pathways, enzymes and resistance-associated genes relevant to your biological question, with database coverage and annotation limitations made explicit.
Recover genomes from communities
Link genomic features to recovered MAGs where the shotgun data support assembly and binning, with completeness and contamination estimates for the resulting bins.
Compare communities in context
Relate community diversity and composition to treatment, environment, host information or time. Combine statistical results and metadata to develop biological interpretations and hypotheses.
Starting your project
What we need from you
Sequencing reads or existing results
FASTQ or FASTQ.gz reads; FASTA contigs or existing MAGs; or processed count/abundance tables for suitable downstream work. Tell us the platform, read layout and processing already performed. For amplicons, include the marker region and primers.
Sample information & research question
A sample sheet matching file names to sample IDs, groups, replicates and relevant covariates. Include controls, batches and paired or longitudinal relationships where applicable. Begin with a project description; data transfer is arranged after discussion.
We can work with Illumina, Oxford Nanopore or PacBio datasets where suitable for the requested analysis. Existing assemblies and tables enter the workflow at the appropriate stage.
Analytical workflow
A typical metagenomics analysis workflow
The stages below describe the available analytical route, not a compulsory linear pipeline. Profiling does not always require assembly, and assembly/MAG recovery applies to shotgun data when included in the project.
01 · Data review & quality control
Check inputs, metadata and read quality
View step details
Review sample IDs, the experimental design and available data. Assess read quality and select preprocessing, including host filtering where appropriate. For processed inputs, review their provenance and suitability.
02 · Taxonomic profiling
Characterize community composition
View step details
For shotgun data, choose suitable read- or contig-based classification. For amplicons, denoise marker reads and assign taxonomy using a suitable reference. Profiling can proceed without metagenome assembly.
03 · Assembly & genome recovery
Recover contigs and MAGs where included
View step details
This optional shotgun branch covers assembly, binning and genome-quality assessment. It is not a step in a standard 16S/18S/ITS workflow. Co-assembly or per-sample assembly is selected for the study rather than assumed in advance.
04 · Functional annotation
Investigate genes and pathway potential
View step details
Where shotgun data or suitable assemblies are available, annotate genes and summarize selected functional categories. Functional inference from marker genes, if specifically agreed, is reported as prediction rather than direct gene measurement.
05 · Statistics & interpretation
Compare samples using the study design
View step details
Quantify suitable features, examine diversity and assess group differences or associations where the design supports them. Account for relevant covariates, repeated observations and multiple testing as appropriate.
06 · Visualization & reporting
Deliver figures, tables, files and methods
View step details
Bring together metadata-linked outputs, publication-oriented figures and the agreed summary report. Discuss the main findings, interpretation and limitations directly.
Project outputs
Deliverables — what you will receive
The quotation specifies the deliverables for your project. An amplicon diversity study and a shotgun MAG-recovery project will produce different files.
Quality summaries & processed data
Read-quality summaries, filtering statistics and agreed processed tables. Cleaned reads or other intermediate files can be included when specified in the scope.
Assemblies & MAG outputs
Where included: FASTA contigs, recovered genome bins, taxonomic assignments and quality summaries. MAG recovery is an analysis objective, not a guarantee of recovering every organism or a fixed number of complete genomes.
Figures & statistical results
Relevant composition plots, heatmaps, diversity comparisons, ordinations and model results. Figure types follow the question and data, with sample metadata and group labels carried through.
Summary report & methods
A structured PDF report describing the tools and versions used, methods, key findings and limitations. Additional methods text, scripts or intermediate outputs are agreed explicitly where required.
Working with Tailoredomics
Why choose our metagenomics services?
Biological context
Analysis is developed around your hypotheses, sample types and experimental design, with the flexibility to begin from raw reads or existing results.
Methods suited to the data
Tools and databases are selected for the analysis required. Their versions and relevant limitations are documented so the results can be understood and assessed.
Direct scientific communication
Discuss the dataset, analytical choices and findings with the person responsible for the analysis. Questions can be clarified throughout the project.
Results prepared for use
Receive organized tables, interpretable figures and clear explanations that support research, collaboration and manuscript preparation.
Research contexts
Applications of metagenomics
Environmental & agricultural microbiology
Study communities in soil, water, marine environments, plant-associated systems and extreme habitats. Explore associations with environmental conditions, nutrient cycling and plant–microbe research questions.
Biotechnology & enzymology
Prioritize candidate enzymes, gene clusters and metabolic pathways for further investigation, including projects concerning biofuels, biodegradation or wastewater treatment.
Food systems & fermentation
Compare microbial populations and functional potential across fermentation stages, ingredients or processing conditions. Investigate sequence evidence relevant to food microbiology research.
Host-associated & comparative research
Explore community shifts across host groups, environments or time points. Where recovered genomes support it, investigate genomic variation and candidate adaptations; associations guide hypotheses rather than establish causality.
Before you enquire
Frequently asked questions
Do you perform sequencing or sample preparation?
Tailoredomics provides downstream bioinformatics analysis of existing data. Sequencing, library preparation and nucleic-acid extraction are arranged through your institution, sequencing core or commercial provider.
What is the difference between shotgun and amplicon analysis?
Shotgun metagenomics samples DNA across the community and can support taxonomic profiling, gene analysis and genome recovery. Amplicon analysis targets markers such as 16S, 18S or ITS and primarily addresses community composition and diversity. Marker choice determines the organisms covered; standard marker assays do not provide a general viral survey.
Which files can I send, and can you use processed results?
We accept raw FASTQ/FASTQ.gz reads from sequencing facilities and can assess FASTA assemblies, existing MAGs or count/abundance tables for suitable downstream work. Include the platform, processing history and relevant metadata. Processed tables cannot recover sequence information that was not retained.
Do I need metadata or a reference genome?
A reference genome is not required for many community analyses. Host filtering may need an appropriate host reference. Sample IDs and study-design information are needed for reliable group comparisons; include replicates, controls, batches and relevant covariates.
Can you guarantee MAG recovery or species-level identification?
No fixed recovery or resolution can be promised before assessing the data. Sequencing depth, community complexity, strain diversity and reference coverage all affect the result. We report supported assignments and genome-quality estimates.
Which tools and databases will you use?
Methods depend on the dataset and question. The service descriptions above give examples; we can also assess required tools or an existing pipeline. Tools and database versions used are documented in the report.
What will I receive, and how long will it take?
Deliverables, price and timing are agreed after reviewing your starting data and requested analyses. Outputs can include processed tables, figures, annotations, assemblies or MAGs and a summary report; only the items included in the scope are promised.
How do I transfer the data?
Start with a description of your project through the enquiry form. You do not need to upload raw reads at first contact. We agree a suitable transfer method, such as an institutional or sequencing-provider download link, after discussing the project.
Further reading
Understand the analyses behind your project
What is metagenomics?
Metagenomics examines genetic material recovered from mixed environmental or biological samples. Shotgun analysis describes community DNA and functional potential; marker-gene analysis provides a complementary, targeted view. Read What Is Metagenomics?.
From reads to MAGs
Learn how assembly, binning and quality assessment relate to genome recovery: Metagenome Assembly Pipeline: From Reads to MAGs.
Understanding community diversity
Explore within-sample diversity and differences between communities: Alpha and Beta Diversity.
Discuss your project
Ready to analyse your metagenomics data?
Tell us about your samples, available files and research question. Whether you need a complete workflow or help with a particular analysis, we can define the scope and suitable deliverables.
Prefer email? info@tailoredomics.com