Senior Bioinformatics Engineer

Senior Bioinformatics Software Engineer

What if the work you did every day could impact the lives of people you know? Or all of humanity? At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients. Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible.

About the Role

We build the software platform that validates DRAGEN—Illumina's secondary analysis engine for clinical and research genomics. Our internal framework orchestrates thousands of automated tests across HPC clusters, AWS, and local DRAGEN nodes, and gives 30+ engineering teams the tooling they need to ship pipeline changes with confidence.

We're hiring a Senior Bioinformatics Software Engineer to expand and maintain this platform. You'll lead verification work in cross-functional teams, drive complex technical initiatives end-to-end, and help shape how clinical-grade genomics gets tested at scale.

What You'll Do

• Lead end-to-end verification for complex data analysis software in multidisciplinary teams.
• Partner with engineering, bioinformatics, pipeline, and scientific stakeholders to turn requirements into traceable, automated verification workflows.
• Design and build scalable platform capabilities—plugin frameworks, workflow orchestration, CI/CD, and observability.
• Lead through code and design review; champion maintainable architecture and engineering standards.
• Improve how we work: documentation, reproducibility, automation, and developer productivity.

  What We're Looking For

  Required

  • Typically requires a minimum of 5 years of related experience with a Bachelor's degree; or 3 years and a Master's degree; or a PhD without experience; or equivalent work experience.
  • Significant Python experience (Django / REST APIs, pytest, modern tooling)
  • Hands-on experience with CI/CD, Git/GitHub, Docker, and Linux/Unix environments
  • Strong software architecture and system design; comfortable owning technical direction across teams

    Strongly preferred

    • Deep experience in NGS or secondary analysis (variant calling, methylation, alignment, etc.) and understanding of oncology, molecular biology, bioinformatics, or related biology.
    • Familiarity with DRAGEN or comparable secondary analysis platforms
    • Running workloads on HPC clusters and AWS
    • Workflow orchestration beyond CI/CD (e.g. Airflow, Nextflow, or similar)
    • Hands-on use of AI coding agents, IDE harnesses, or LLM tool integrations (including MCP) to ship features, automate engineering workflows, or build internal tooling
    • Using AI for code review, test design, refactoring, or documentation—with examples of projects or workflows you have delivered with AI-assisted development, not just ad hoc experimentation
    • Open-source contributions in bioinformatics or developer tools

      Why This Role

      • Real impact on clinical genomics. Our tests gate releases that go into hospitals and labs worldwide.
      • Hard problems. Clinical-grade reproducibility, massive test matrices, multi-cloud, regulated environments — all in one role.
      • Scope. Grand scope across ~30 repos, hundreds of test suites, and dozens of engineers. Your architectural decisions compound.
      • Growth. Clear path to Staff Engineer, depending on your interests.