Pipeline development & reproducibility

We develop production-grade, tested pipelines using Nextflow, Snakemake or CWL and follow community standards (nf-core where applicable). Pipelines are containerised (Docker / Singularity), dependency-managed (Conda/Bioconda), versioned and accompanied by CI tests, sample manifests and example datasets so you can reproduce every run.

• Modular design and tests for unit/edge-case validation.
• Provenance capture and automatic checkpoints for resumability.
• Support for WGS/WES, RNA-seq, targeted panels and custom assays.

AI‑assisted variant interpretation & annotation

We integrate annotation tools and knowledge-bases (VEP/ANNOVAR, dbNSFP, ClinVar, gnomAD) with machine-learning models to prioritise variants and extract candidate biomarkers. Our service includes evidence aggregation, automated ACMG-style scoring support and human-in-the-loop review workflows for clinical and translational use cases.

• Custom annotation stacks, phenotype-driven prioritisation and model explainability.
• Support for somatic and germline variant interpretation and tumor/normal analyses.

Cloud deployment & infrastructure

We architect and deploy pipelines to AWS, Google Cloud, Azure or on-prem Kubernetes with secure VPCs, IAM, private endpoints, and encryption-at-rest/in-transit. Implementations include autoscaling compute, spot/preemptible cost optimization, storage lifecycle policies, and integration with object stores (S3/Blob).

• Reference architectures using managed services (Batch, Genomics APIs, Kubernetes, Terraform/CloudFormation).
• CI/CD for pipeline releases, image registries and automated integration tests.
• Options for hybrid cloud or fully air‑gapped deployments for regulated environments.

Single‑cell & multi‑omics

End-to-end preprocessing, QC and downstream analysis for single-cell RNA-seq, multi-omics integration and spatial transcriptomics. Services include cell calling, doublet detection, normalization, clustering, differential expression, integration across batches and publication-ready visualisation.

Metagenomics & pathogen surveillance

Deployable pipelines for taxonomic classification, abundance estimation, assembly, and antimicrobial resistance (AMR) profiling. Suitable for public-health surveillance and environmental sequencing, with contamination filtering, reference updates and reporting suited for outbreak analysis.

Validation, benchmarking & regulatory readiness

We perform technical validation and benchmarking using standard datasets (GIAB, simulated truth sets) and produce documentation, runbooks and traceable evidence required for regulated use (CLIA, GxP) or for clinical research workflows.

Custom tooling, APIs & visualisation

We build web apps, APIs and dashboards that expose pipelines to scientists and stakeholders. Features include job submission UIs, interactive QC dashboards, variant review interfaces, and programmatic endpoints for integration with LIMS, ELN or clinical systems.

Security, data governance & compliance

Security is integral: role-based access control, encryption, audit logging, data de‑identification and consent-aware data handling. We can help implement governance aligned with GA4GH standards, HIPAA, GDPR and other regional requirements.

Managed analysis & support

Operate routine runs on your behalf, with monitoring, incident response, data lifecycle management and SLAs. Options include flat-rate managed services, burst capacity on demand, or a handover model where we deliver reproducible pipelines and documentation for your team to operate.

DevOps, CI/CD and reproducibility

We implement CI for pipelines (linting, unit tests, integration tests on small datasets), automate container builds, and maintain versioned releases so analysis is reproducible and auditable over time.

Engagement process

1. Discovery & scoping — data, timelines, success metrics.
2. Technical specification & prototype — reproducible PoC on sample data.
3. Implementation & validation — CI tests, benchmarking and documentation.
4. Deployment, handover or managed operation — runbooks, training and support.