Senior Bioinformatics Software Engineer — Genomics Platform

Illumina; San Diego (CA); Hybrid; USD 129,000 - 194,000; Full time

Job summary

Illumina in San Diego, CA seeks a Senior Bioinformatics Software Engineer to expand and maintain DRAGEN platform verification. You will lead cross‑functional verification efforts across HPC clusters, AWS, and local nodes, shaping how clinical genomics tests are validated at scale.

You will drive end-to-end technical initiatives, design scalable workflows, and mentor teams while upholding maintainable architecture and high engineering standards to deliver reliable, reproducible results.

Qualifications

• Minimum five years of related experience with a Bachelor's degree; or 3 years with a Master's; or PhD without 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 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 (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

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.

Skills

Python

CI/CD

Git/GitHub

Docker

Linux/Unix

Software architecture

Education

Bachelor's degree

Master's degree

PhD (no experience)

Equivalent work experience

Tools

Django

REST APIs

pytest

GitHub

Job description

Illumina in San Diego, CA seeks a Senior Bioinformatics Software Engineer to expand and maintain DRAGEN platform verification. You will lead cross‑functional verification efforts across HPC clusters, AWS, and local nodes, shaping how clinical genomics tests are validated at scale.

You will drive end-to-end technical initiatives, design scalable workflows, and mentor teams while upholding maintainable architecture and high engineering standards to deliver reliable, reproducible results.