Bioinformatics Engineer - Oncology & Hematology

SeqOne Inc.; Montpellier, Paris; Hybrid; EUR 50,000 - 75,000; Full time

Benefits offered by this job

Hybrid work options

Flexible hours

Health insurance

Competitive benefits

Job summary

SeqOne Inc. in Montpellier/Paris/Cambridge seeks a Bioinformatics Engineer to design, build and operate production-grade bioinformatics applications and pipelines.

You will partner with research and product teams to translate scientific needs into reliable software, lead code quality efforts and ensure analyses are reproducible and scalable. The role combines research with software engineering, emphasizing pipelines, CI/CD and collaborative publications, with hybrid work options across multiple

Qualifications

• Master’s degree in Bioinformatics, CS or related field and 2+ years of bioinformatics development.
• Strong Python, UNIX/Linux and Bash proficiency.
• Experience with Snakemake and Nextflow workflow managers.
• Familiarity with Git and Docker for reproducible environments; good communication and teamwork.

Responsibilities

• Design and build tools and pipelines for complex biological data.
• Maintain and improve applications; troubleshoot user issues.
• Optimize performance; ensure reproducible and robust results.
• Collaborate with scientific teams; contribute to publications and presentations.
• Lead code reviews; enforce coding standards and secure practices.
• Track new methods/technologies and integrate them when relevant.
• Document and train users and teammates.

Skills

Python

UNIX/Linux

Bash

Workflow management

Communication

Teamwork

Problem solving

Education

Master's degree in Bioinformatics or CS

PhD or equivalent (nice to have)

Tools

Snakemake

Nextflow

Git

Docker

CI/CD (GitLab/GitHub Actions)

HPC/Cloud (SLURM, AWS/GCP/Azure)

Job description

Permanent, full-time Hybrid, Hub-Based

Bioinformatics Engineer - Oncology & Hematology

About SeqOne

SeqOne develops next-generation genomics software that turns complex sequencing data into clear, actionable insights for clinicians and researchers. Our platforms power high-impact applications in oncology and rare disease, with a strong focus on robustness, reproducibility, and speed. We are building a world-class team in Montpellier (FR), Paris (FR), and Cambridge (UK).

Why SeqOne?

• Direct Impact: Your contributions will enhance customer experience and shape the evolution of our genomic products.
• Stimulating Environment: Passionate team, innovative projects, and a culture of transparency.
• Flexibility: Remote work options, flexible hours, and competitive benefits.
• Growth Opportunities: Internal career development, continuous training, and participation in scientific conferences.
• Soft Skills: "Unstoppable Positivity" (resilience and solution-first mindset) and "Open Heart, Hands-On" (kindness combined with direct feedback).

Tasks

As a Bioinformatics Engineer, you will design, build, and operate production-grade bioinformatics applications and pipelines. You will partner with research and product teams to translate scientific needs into reliable software, lead code quality efforts (reviews, testing, CI/CD) and help the team adopt best practices so that complex analyses become routine, reproducible and scalable.

• Design and develop tools and pipelines for complex biological data.
• Maintain and improve existing applications while troubleshooting and resolving user issues.
• Optimize performance and reliability, ensuring reproducible and robust results.
• Collaborate closely with scientific teams and contribute to publications and presentations.
• Lead code reviews, enforce coding standards and secure practices.
• Track new methods/technologies and integrate them when relevant.
• Share knowledge through documentation creation, training and guidance for both users and teammates.

Requirements

• We are seeking candidates with a Master’s degree (Bac+5) in Bioinformatics, CS or a related field and at least 2 years of experience in bioinformatics development.
• Strong proficiency in Python, UNIX/Linux, and Bash is required.
• Experience with Workflow managers (Snakemake, Nextflow).
• Familiarity with Git (branching, PRs, code reviews) as well as Docker for creating reproducible environnements is essential.
• Candidates should demonstrate clear communication skills, the ability to effectively in a team, autonomy in managing tasks and strong analytical problem-solving abilities.

Nice to have

• A PhD or equivalent research experience is a plus.
• Experience with CI/CD pipelines (GitLab CI, GitHub Actions) is advantageous.
• Knowledge of environment managers such as pyenv, poetry or virtual environments, as well as experience with HPC or Cloud (SLURM, AWS/GCP/Azure) is a strong asset.
• Proficiency in additional programming languages sur as R, Perl, Groovy, Nim or Rust is welcomed.

Benefits

Bases in Montpellier / Paris or Cambridge
Fixed salary, bonus, free health insurance
This position offers flexible working arrangements, including hybrid, on-site, or full remote options