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Services

Three areas of practice, delivered end to end

Each engagement is scoped to your data, infrastructure, and team — not delivered from a fixed catalogue. Initial conversations are free and confidential; written quotes follow within a week.

Service 01 · Pipeline engineering

Custom pipelines, built around your data.

From a single bash script to a full Nextflow workflow — pipelines that fit your existing infrastructure and pass the scrutiny of a regulated environment.

We design, implement, validate, and document. The pipeline you receive runs reproducibly, has tests that prove it works, and comes with a runbook the next person on your team can actually follow.

Nextflow Snakemake Docker Singularity HPC Validation
What's included

From design through to handover.

Every engagement covers the full lifecycle — not just the code.

Pipeline design
Scoped to your sample type, sequencing platform, and analytical question.
Implementation
In Nextflow, Snakemake, or your team's existing framework.
Containerisation
Docker or Singularity images for reproducible, environment-independent execution.
Validation runs
Against reference data with documented expected outputs.
Runbook & docs
Parameter reference, troubleshooting guide, and expected-output catalogue.
Compute integration
HPC scheduler, local server, or air-gapped environment — configured to fit.
Handover session
Live walkthrough with the team who will run and maintain the pipeline.
Support window
A defined period after delivery for questions, bug reports, and small tweaks.
How we work

Four stages, no surprises.

Typical engagements run 2–8 weeks. Fixed-price for well-defined pipelines; day-rate for exploratory or ongoing work.

  1. 01
    Scoping call

    A short call to understand your data, your question, and the constraints you're working within. Free and confidential.

  2. 02
    Written proposal

    A clear quote with deliverables and timeline, typically within a week of the first call.

  3. 03
    Build & validate

    Iterative development with regular updates. Validation runs against your reference data before sign-off.

  4. 04
    Handover

    Documentation, training session, and a defined support window for follow-up.

Service 02 · Data processing

Sequencing data in, annotated reports out.

End-to-end processing of microbial sequencing data — from raw FASTQ to clinically interpretable reports, on UK-sovereign infrastructure with full chain of custody.

If you have reads and you need answers, this is the service. We accept Illumina or Nanopore data via encrypted upload, run the appropriate pipelines, and return self-contained HTML reports — typically within days of sample arrival.

Illumina Nanopore Bacterial WGS Amplicon AMR Phylogenetics Outbreak
What we handle

Routine and bespoke microbial analyses.

From single-isolate WGS through to outbreak-scale phylogenetic reconstruction.

Bacterial WGS
Isolate genomes — species, MLST, AMR profile, virulence, and species-specific typing.
16S / ITS amplicons
Mixed communities — taxonomic composition, abundance, and diversity metrics.
Outbreak investigation
Phylogenetic placement, SNP-based clustering, and transmission analysis.
AMR surveillance
Batch processing of isolate collections with summary outputs for reporting.
Custom analyses
Where existing pipelines don't fit your sample type, primer set, or question.
Re-analysis
Previously generated data revisited with updated databases or methods.
Quality assessment
Independent verification of upstream pipeline outputs.
Interpretation
Optional handover call to walk through findings and answer questions.
How it works

From sample to report.

Encrypted transfer, sovereign UK processing, self-contained deliverables.

  1. 01
    Scoping

    Discuss sample type, expected scope, and turnaround.

  2. 02
    Quote

    Written quote with per-sample or per-batch pricing, within a week.

  3. 03
    Encrypted transfer

    FASTQ data uploaded via the NS Bio portal — encrypted in transit and at rest.

  4. 04
    Processing

    Run on sovereign UK infrastructure with AES-256 encryption and a documented audit trail.

  5. 05
    Delivery

    Self-contained HTML reports plus optional raw outputs (assemblies, BAMs, VCFs).

  6. 06
    Handover

    Optional walkthrough call. Methods documentation suitable for publication or audit.

See it in action

Flagship pipelines with worked examples.

→ /pipelines

Two flagship pipelines, each with example reports.

The bacterial WGS and 16S / ITS amplicon pipelines are documented with worked examples from public Nanopore data — the exact format of report you'd receive. Custom analyses are scoped on request.

Bacterial WGS → 16S / ITS amplicon → Discuss a custom analysis →
Service 03 · Training

Microbial bioinformatics training, for your team.

Off-the-shelf bioinformatics courses rarely match the mix of backgrounds and tools on a real laboratory team. Our sessions are scoped after a discovery call.

The right amount of time is spent on the basics, the right depth is reached on the bits you'll actually use, and you walk away with hands-on materials you can revisit. Delivered in person, remote, or hybrid.

NGS basics Nanopore Phylogenetics Biopython Reproducibility Long-read
Formats

From a half-day refresher to a full course.

Every format is scoped against your team's existing skills and the tools you actually use.

Half-day refresher
Targeted topic, ~3 hours — useful for a single tool or technique.
Single-day workshop
Six hours of structured content with hands-on exercises and breaks.
Multi-day course
Two to five days, deeper dive built around extended hands-on work.
Topic-specific
For example, "Setting up Nanopore basecalling for clinical use".
Remote delivery
Synchronous over video conference with shared exercise environments.
Hybrid
In-person with remote attendees joining live; recordings on request.
One-to-one
For specialists joining a microbial bioinformatics group.
Custom curriculum
Designed from scratch against your team's workflows and skill mix.
What's included

Materials you keep.

All training comes with reference materials you can revisit and a follow-up support window.

Discovery call
A short conversation to scope the right level and content for your team.
Custom materials
Slides and exercises referencing your tools, your data, and your workflows.
Hands-on datasets
Worked exercises with provided sample data — runnable on a laptop.
Reference cards
Single-page cheat-sheets for the tools and commands covered.
Follow-up window
A defined period (typically four weeks) for follow-up questions by email.
Recordings
Session recordings provided where the format allows it.
Who it's for

Teams adopting or scaling NGS work.

Lab teams
Transitioning from Sanger to next-generation sequencing.
New bioinformaticians
Specialists joining a microbial genomics group from an adjacent field.
Nanopore adopters
Research teams running Oxford Nanopore for the first time.
Public-health staff
Interpreting pipeline outputs for surveillance or outbreak response.
Sovereignty

All work on sovereign UK infrastructure.

Every engagement — whether pipeline development, data processing, or training — runs on NS Bio's self-hosted UK infrastructure. Data never leaves the United Kingdom; processing is encrypted at rest and in transit; chain of custody is fully documented. Reports are self-contained HTML files with no CDN dependencies and no analytics.

Have a project
you'd like to talk through?

Initial conversations are free and confidential. Most projects begin with a short scoping call — followed by a written quote within a week.

Start a conversation → Request a quote