Backend Bioinformatics Engineer

Il y a 14 minutes

Montpellier, Occitanie, France SeqOne Genomics Temps plein

Mission

Design, evolve, and industrialize production bioinformatics pipelines and the associated backend services to improve reliability, turnaround time (TAT), traceability, and operability of analyses.

Key Responsibilities1) 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 SkillsBioinformatics 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 Types: Full-time, Permanent

Pay: From 50,000.00€ per year

Work Location: Hybrid remote in 34000 Montpellier

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