- Company Name
- INRAE Occitanie-Toulouse
- Job Title
- Ingénieur-e en bio-informatique
- Job Description
-
**Job Title**
Bioinformatics Engineer
**Role Summary**
Design, maintain, and extend bioinformatics pipelines for high‑throughput sequencing (RNA‑seq, amplicon) data to identify and characterize grapevine viral genomes. Develop analytical workflows in R and Python, oversee batch processing on SLURM clusters, and implement robust data management and quality control procedures across the virome research program.
**Expactations**
- Deliver reproducible, well‑documented analysis pipelines on a Linux HPC environment.
- Collaborate closely with virology and genomics teams and disseminate findings efficiently.
- Maintain data integrity, version control, and comply with data governance best practices.
**Key Responsibilities**
- Maintain and evolve an existing Nextflow pipeline for viral genome assembly from RNA‑seq data.
- Design, code, version, document, and maintain new bioinformatics workflows (Nextflow, Snakemake).
- Develop and automate data processing, statistical analyses, visualizations, and report generation in R and/or Python.
- Launch and supervise analyses on a SLURM‑based compute cluster; manage job scheduling, resource allocation, and log monitoring.
- Implement a data management plan: validate data quality, ensure integrity, create traceable backup pipelines, and populate databases.
- Navigate large public sequencing repositories (SRA, ENA) to retrieve reference datasets and metadata.
**Required Skills**
- High‑throughput sequencing data handling, including viral genome assembly.
- Workflow engines: Nextflow or Snakemake (extensive experience preferred).
- Linux scripting (Bash), SLURM cluster management, job scripting, and resource monitoring.
- Container technologies: Singularity/Apptainer or Docker.
- Source control: Git, versioning, branching, pull requests.
- Programming: proficiency in Python (preferred) and/or R for data analysis, visualization, and reporting.
- Basic scientific English for literature review and documentation.
**Required Education & Certifications**
- Master’s or Engineering degree (Bac+5) in Bioinformatics, Computational Biology, Genomics, or related field, or equivalent professional experience.
- Demonstrated expertise in bioinformatics pipeline development and high‑throughput sequencing analysis.