Automated Testing Framework for Genomic Pipelines
SequoiaAT built domain aware automation for a high throughput genomics platform. Release time dropped from six weeks to two. Teams ship with confidence and clear traceability.
About the client
A global genomics innovator that derives insight from patient tissue data using modern pipelines. Prior to SequoiaAT engagement, testing and release steps were mostly manual and slow.
Challenges
- Manual testing across many steps stretched to six weeks
- Validation needed six to eight domain specialists
- Reproducibility was hard to prove without automation
- Complex bioinformatics checks needed deep scientific review
Solution at a glance
- Custom framework from FASTQ to report verification
- Bioinformatics experts embedded with test engineers
- CI and CD with container based runs and parallel jobs
- Automatic exports, logs, and requirements traceability
What we built
Custom automation framework
Stage wise checks cover parsing, alignment, variant calls, annotation, and reports. Data is verified end to end.
Domain expert reviews
Bioinformaticians guide validation logic for allele frequency limits, coverage metrics, and sample quality flags.
CI and CD integration
Tests run on each commit. Jenkins was used first then moved to GitHub Actions for container runs and scale out.
Documentation and traceability
Exports include logs and coverage views. Requirements map cleanly to test designs and cases.
Why SequoiaAT
Domain mastery
Strong grasp of genomic data rules gives meaningful checks that align with clinical goals.
Ownership
Single team for design, automation, CI and CD, and reporting. Clear responsibility and faster fixes.
Built for scale
Custom code avoids waste. Parallel runs keep flow quick as assays and references grow.
Where we work in Europe
We support genomic test automation across leading hubs in Europe including Cambridge, Oxford, London, Basel, Zurich, Lausanne, Berlin, Munich, Paris, Lyon, Amsterdam, Copenhagen, Stockholm, Helsinki, Barcelona, Madrid, and Dublin. Teams get the same CI and CD rigor, reproducibility, and traceability with local time zone collaboration.