Senior Bioinformatics Engineer

Illumina • San Diego, CA

3d • Hybrid

About The Position

Illumina is hiring a Senior Bioinformatics Software Engineer to expand and maintain the software platform that validates DRAGEN, Illumina’s secondary analysis engine for clinical and research genomics. The internal framework orchestrates thousands of automated tests across HPC clusters, AWS, and local DRAGEN nodes, and provides tooling used by more than 30 engineering teams.

The role leads verification work in cross-functional teams, drives complex technical initiatives end to end, and helps shape how clinical-grade genomics is tested at scale. Responsibilities include turning requirements into traceable automated verification workflows, building scalable platform capabilities, and improving documentation, reproducibility, automation, and developer productivity. The position has broad scope across repositories, test suites, and engineering teams, with a potential growth path to Staff Engineer depending on the employee’s interests.

Requirements

• Typically, at least 5 years of related experience with a Bachelor’s degree, 3 years with a Master’s degree, a PhD without experience, or equivalent work experience.
• Significant Python experience, including Django or REST APIs, pytest, and modern tooling.
• Hands-on experience with CI/CD, Git/GitHub, Docker, and Linux/Unix environments.
• Strong software architecture and system design skills, with the ability to own technical direction across teams.

Nice To Haves

• Deep experience in NGS or secondary analysis, such as variant calling, methylation, or alignment, and understanding of oncology, molecular biology, bioinformatics, or related biology.
• Familiarity with DRAGEN or comparable secondary analysis platforms.
• Experience running workloads on HPC clusters and AWS.
• Experience with workflow orchestration beyond CI/CD, such as Airflow or Nextflow.
• 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.
• Experience using AI for code review, test design, refactoring, or documentation, with examples of delivered projects or workflows.
• Open-source contributions in bioinformatics or developer tools.

Responsibilities

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

Benefits

• Variable cash program (bonus or commission) eligibility for all employees; eligible roles may also receive equity.
• Access to genomics sequencing.
• Family planning benefits.
• Health, dental, and vision benefits.
• Retirement benefits.
• Paid time off.
• Employee Resource Groups offering career development experiences, cultural awareness, and social responsibility engagement opportunities.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior