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Sr Staff Software Engineer, Clinical Genomics

Company: Illumina
Location: San Diego
Posted on: May 18, 2019

Job Description:

Illumina is seeking a Sr. Staff Software Engineer to join the Clinical Genomics Software Engineering team, where we are improving human health by unlocking the power of the genome. By pairing high throughput sequencing of DNA with advanced algorithms, we are enabling clinicians and pathologists around the world to provide personalized diagnoses and treatments to cancer patients.

As a software engineer, you will develop algorithms for next-generation sequencing, bioinformatics pipelines, integration with instrument control software, filtering, annotation and reporting. The ideal candidate will enjoy working in a fast-paced and dynamic environment and be intrinsically driven to both create high-quality and high-performing software and affirming its quality through simulation testing, unit and integration testing, design specifications, and collaboration with the team on verification testing and refining requirements.

Join one of biotech's most successful companies to create world-class software with the best and brightest in the industry. You will work in an environment that is collaborative, innovative and fun. As an Illumina Sr. Staff Software Engineer, you will enjoy a rich network of bioinformatics scientists, software engineers and test engineers to accelerate your work.


  • Work as part of Agile scrum teams to design and implement clinical-grade bioinformatics pipelines and patient-focused sequencing portals
  • Work closely with bioinformaticians and software engineers to develop novel algorithms
  • Deliver software architecture, design specifications and implementations
  • Integrate new pipelines and products with new and existing Illumina platforms
  • Maintain rigorous quality and performance standards
  • Participate in requirement, hazard, design and code reviews
  • Develop software that solves the problem at hand with an eye toward performance, extendibility and maintainability
  • Collaborate with product owners, , test engineers, systems analysts, scientists, and stakeholders to create a robust product that suits the users' needs


    • Bachelor of Science degree or higher in Computer Science, Bioinformatics, Computational Biology or related field

      Required Skills & Experience

      • BSc/MS: 8-12+ years of experience or PhD: 4-7+ years of experience
      • Experience in an object-oriented programming language such as C++, Python, Java or C# (C++, Python preferred)
      • Experience with scripting languages, including Python, bash, R, Perl
      • Experience programming in a Linux environment
      • Algorithm development experience
      • Expertise in software engineering best practices
      • Dedicated to creating software with the utmost quality standards
      • Excellent problem solving, troubleshooting and communication skills
      • Excellent technical writing skills in English
      • Working knowledge of Linux

        Preferred Skills & Experience

        • Advanced degree in bioinformatics or computer science
        • Experience developing software for next-generation sequencing or genomics applications
        • Have an understanding of oncology, molecular biology, bioinformatics, or related field of biology
        • Probability and statistics
        • Experience writing design specifications for medical device software
        • Experience writing multi-threaded algorithms
        • Parallel or distributed computing; big data processing
        • Experience with Docker, Git, Visual Studio, .NET Core
        • HPC or cluster computing

          Illumina believes that everyone has the ability to make an impact, and 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. If you have a disability or special need that requires accommodation, please contact us at To learn more, visit:

Keywords: Illumina, San Diego , Sr Staff Software Engineer, Clinical Genomics, IT / Software / Systems , San Diego, California

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