Custom NGS Pipeline Development
NGS pipelines that are built and verified.
We develop custom analysis pipelines for molecular pathology labs, biotech and pharma R&D. What typically takes an in-house expert months, we deliver as a robust, reproducible pipeline ready for routine use.
The key difference: we do not only implement. We independently verify correctness and output integrity. With a single in-house bioinformatician (or an AI-generated pipeline), you often cannot be sure whether results are correct. We combine engineering and deep NGS expertise to ensure your pipeline runs reliably and produces the intended output.
What you get
- Pipeline implementation tailored to your assay and environment
- Reproducible execution (versioned, documented, portable)
- Verification of correctness with defined acceptance criteria
- Stable outputs suitable for routine operations and reporting
Why teams hire us
- internal expert time is scarce
- you need confidence in correctness, not just "it runs"
- you want predictable delivery and clean handover
- you need a partner who speaks lab and engineering
What we deliver
Depending on your needs, deliverables can include a full end-to-end workflow, modular pipeline components, standardized reports, and integration into your compute environment.
- End-to-end workflows (QC to analysis to standardized results and reporting)
- Refactoring from scripts into maintainable, testable software
- Deployment on HPC or cloud, with reproducible environments
- Documentation (usage, parameters, assumptions, limitations)
- Test strategy and automated checks for stability and regressions
How we work
- Scoping - requirements, assay, inputs/outputs, success criteria
- Implementation - pipeline development on representative data
- Verification - independent checks, acceptance tests, edge cases
- Handover - documentation, deployment support, optional maintenance
Typical inputs: assay and platform, expected sample volume, compute environment (HPC/cloud), and a small representative dataset (if available).
Service request
For a fast and accurate estimate, include:
- assay and platform
- sample count / data size
- desired outputs (tables, VCF, report)
- target environment (HPC/cloud)
- timeline
Example application areas
We build analysis workflows for a broad range of NGS assays. A selection:
Genomic variation
- Whole-genome, whole-exome or targeted panels
- Variant calling and annotation
- Structural variants and rearrangements
- Somatic analyses in oncology
- Trio/cohort/pedigree analyses
Transcriptomics
- Differential expression (genes / isoforms / exons)
- Fusions, circular RNAs, trans-splicing
- Long non-coding RNA detection
- RNA editing, exon retention, alternative polyadenylation
Epigenetics
- Bisulfite sequencing workflows
- Differentially methylated regions
- Non-CpG and hydroxymethylation analysis
- Allele-specific methylation / imprinting
- Integration with TF binding and histone marks