Senior Bioinformatics Engineer

About the role

Qualifications

• 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
• 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.
• We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact [email protected]. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship.

Preferred Qualifications

• Strongly preferred
• The estimated base salary range for the Senior Bioinformatics Engineer role based in the United States of America is: $129,400 - $194,000. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. The range reflects long‐term growth in the role; therefore, most candidates are hired between the minimum and middle of the range. Placement depends on experience, skills, location, and internal equity. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.

Responsibilities

• 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
• 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.
• #LI-HYBRID
• The estimated base salary range for the Senior Bioinformatics Engineer role based in the United States of America is: $129,400 - $194,000. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. The range reflects long‐term growth in the role; therefore, most candidates are hired between the minimum and middle of the range. Placement depends on experience, skills, location, and internal equity. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.
• We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact [email protected]. To learn more, visit: https://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf. The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship.