Backend Bioinformatics Engineer

Full-time, Permanent Hybrid / Remote (Hub-based)

Backend Bioinformatics Engineer

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).