Senior Bioinformatics Engineer

Illumina•San Diego, CA

About The Position

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.

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.

Nice To Haves

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.

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.