Design, evolve, and industrialize production bioinformatics pipelines and the associated backend services to improve reliability, turnaround time (TAT), traceability, and operability of analyses.
Key Responsibilities
1) Pipeline Development & Industrialization
- Develop and maintain production bioinformatics pipelines (e.g., FASTQ → BAM, BAM → VCF, VCF → annotated VCF) with a high standard of quality, reproducibility, and robustness.
- Contribute to major refactoring initiatives (e.g., modularization, standardization, pipeline tracing, and performance optimization).
- Build and maintain testing and validation capabilities (test datasets, QA reports, regression testing, automation).
2) Backend & APIs (Platform / Service Orientation)
- Design and implement orchestration and backend components for distributed analysis execution: job scheduling, dependency management, launching, tracking, and exposing outputs (e.g., APIs/endpoints, internal services, asynchronous jobs).
- Improve observability (logs, Prometheus metrics, Grafana dashboards, trace collection) and maintainability(clean architecture, managing technical debt).
- Collaborate with DevOps/Infra on CI/CD, Cloud execution, and resource management.
3) Interfaces & Coordination (Subsystem Responsibilities)
- Work closely with stream-aligned teams and other subsystems (e.g., Knowledge, AI Core, BioScience) on interface contracts: inputs/outputs, SLAs, formats, versioning.
- Maintain a clear technical backlog (e.g., Notion/GitLab) with concise, pragmatic specs and consistent prioritization.
Expected Deliverables (Examples)
- Stable, tested, observable pipelines with controlled turnaround time (TAT).
- Reusable validation assets: test datasets + QA reports + validation plans.
- Documented, versioned backend APIs/services with monitoring in place.
- High-quality documentation and traces aligned with quality/regulatory expectations.
Required Skills
- Bioinformatics Core
- Strong mastery of NGS concepts and formats (FASTQ/BAM/VCF, annotation, QC, reproducibility).
- Ability to investigate discrepancies (data, algorithm, implementation) and deliver robust fixes.
- Experience with Nextflow or similar workflow engines.
- Backend Engineering (Key Target of the Role)
- Experience designing backend services (APIs, async processing, orchestration, queues/jobs).
- Solid software engineering practices (testing, CI, refactoring, pragmatic design).
- Strong production mindset: performance, observability, reliability.
- Familiarity with database optimization (e.g., Cassandra, PostgreSQL) and time-series data, metrics storage, or observability data pipelines.
- Collaboration & Organization
- Clear communication across interfaces, dependencies, and trade-offs.
Profile
- Degree in bioinformatics / computer science / related field.
- Significant experience in production environments (pipelines + software engineering).
- Hybrid profile: scientific rigor in approach, engineering excellence in execution.
Nice to Have
- Knowledge of regulatory/RAQA requirements in production systems.
Job Type: Full-time, Permanent
Pay: From 50,000.00€ per year
Work Location: Hybrid/Remote. Company based in Montpellier, France (34000).
