Illumina

Senior Bioinformatics Engineer

Reposted 7 Days Ago

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San Diego, CA, USA

In-Office

129K-194K Annually

Senior level

Healthtech • Biotech

The Role

The Senior Bioinformatics Engineer will design, develop, and maintain backend bioinformatics systems to support genomic analysis, ensuring scalability and reliability, while mentoring junior engineers and collaborating with cross-functional teams.

Summary Generated by Built In

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.

Senior Bioinformatics Engineer – Bioinformatics Platforms & Automation

Are you interested in building the bioinformatics platforms that power large‑scale genomic analysis? At Illumina, we are advancing genomics across research and clinical applications, and we are seeking a Senior Bioinformatics Engineer to design, build, and operate backend bioinformatics systems supporting DRAGEN and related bioinformatics software.

This role is a hands‑on development position focused on building bioinformatics automation, QC systems, and compute infrastructure that enable developers and scientists to move faster and with confidence. It combines bioinformatics expertise, software engineering, and systems ownership, and directly supports some of Illumina’s most business‑critical workflows.

Responsibilities

Design, develop, and maintain backend bioinformatics platforms that support automated QC, validation, and large‑scale analysis workflows across the DRAGEN bioinformatics ecosystem.
Build and evolve internal bioinformatics automation frameworks used for system‑level validation, regression testing, and data quality assessment.
Develop and maintain infrastructure components such as job orchestration, queuing, and scheduling systems used to manage DRAGEN compute workloads.
Partner closely with software engineers, bioinformatics developers, and domain experts to define requirements and deliver robust, scalable backend solutions.
Design, implement, and improve bioinformatics algorithms and QC logic related to sequencing data processing.
Provide operational ownership of bioinformatics compute environments, including troubleshooting failures, debugging system issues, and improving reliability and observability.
Enable and unblock developers by providing tooling, infrastructure support, and deep system knowledge across multiple teams.
Leverage modern AI‑assisted development tools (e.g., intelligent code assistants, workflow automation, and agent‑based tooling) to accelerate development, debugging, and system evolution.
Establish and promote best practices for backend development, bioinformatics automation, testing, and CI/CD.
Participate in design reviews, code reviews, and cross‑functional technical discussions.
Mentor junior engineers and contribute to a culture of technical excellence and continuous improvement.

Requirements

Strong experience developing backend software in a high‑level language such as Python, with solid software engineering fundamentals (data structures, design patterns, testing, maintainability).
Experience building or maintaining backend systems for data processing, automation, or infrastructure‑heavy workflows.
Background in bioinformatics, genomics, molecular biology, or a closely related computational field.
Hands‑on experience working in Linux environments, including scripting and debugging distributed systems.
Experience with job scheduling, queuing systems, or workflow orchestration (e.g., SLURM or similar concepts).
Familiarity with CI/CD pipelines, automation, and production support practices.
Experience using or interest in AI‑assisted software development tools to improve developer productivity and system quality.
Ability to work independently, manage ambiguity, and own complex systems spanning software, data, and infrastructure.
Strong communication skills and a collaborative, service‑oriented mindset.

Preferred Qualifications

Experience with NGS pipelines, DRAGEN, or large‑scale genomic data processing.
Experience building internal platforms or developer tooling.
Exposure to compute fleet operations, on‑prem or hybrid infrastructure, or regulated environments.
Experience mentoring engineers or leading technical initiatives.

Education & Experience

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.

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.

Skills Required

Strong experience developing backend software in Python
Experience building or maintaining backend systems for data processing
Background in bioinformatics, genomics, or a related field
Hands-on experience working in Linux environments
Experience with job scheduling or workflow orchestration
Familiarity with CI/CD pipelines and automation
Experience using AI-assisted software development tools
Ability to manage ambiguity and complex systems

Illumina Compensation & Benefits Highlights

The following summarizes recurring compensation and benefits themes identified from responses generated by popular LLMs to common candidate questions about Illumina and has not been reviewed or approved by Illumina.

Healthcare Strength — Health coverage includes comprehensive medical (HMO/PPO), dental, vision, mental health, life, and disability insurance with options such as FSAs/HSAs and wellness resources. Offerings are described as robust across regions with customization in certain locations.
Leave & Time Off Breadth — Time-off programs include flexible schedules and remote work, PTO or flexible time off, paid holidays and sick leave, and volunteer time. Company-wide shutdowns during summer and winter add additional paid time away.
Parental & Family Support — Family-focused programs include fertility assistance, adoption assistance, and reproductive health support alongside family medical leave. Paid parental leave is provided, with specifics varying by country and employment status.