Principal Software Engineer 1 – Bioinformatics Job in California


  • Our engineering team specializes in developing a fast and accurate FPGA-accelerated platform called DRAGEN, for the secondary analysis of NGS data.
  • Team activities are two-fold: 1) algorithm design of analysis methods to discover variants, and, 2) highly-efficient HW/SW implementation for fast run time.
  • The platform covers a wide range of pipelines, WGS and targeted (enriched/amplicon) germline, WGS and targeted somatic (T/N and tumor-only), DNA/RNA, small variants, CNV and structural variants.
  • The candidate will be able to contribute to the software code base, based on proficient C/C++ programming skills.
  • Our team develops DNA/RNA analysis solutions for use by researchers and clinicians worldwide, which provide sample-to-answer pipelines with high reliability, speed, and completeness of results. The applications are many, from rare and undiagnosed inherited diseases, to population-scale genetics, to cancer.


  • Design, develop, debug and integrate optimized C/C++ software on Linux for multi-threaded applications.
  • Work on FPGA PCIe boards in a Linux environment.
  • Closely interact with bioinformatics and FPGA design teams.
  • Occasionally provide technical assistance to escalated production issues
  • Collaborate with product teams to design, code, and maintain, high quality software against established processes in a scrum team setting
  • Maintain awareness of industry trends and evaluate applicability of new software technologies to platform development efforts
  • Provide technical leadership to an Agile team if required


  • Extensive knowledge and experience with C/C++, multi-threading and memory management techniques.
  • Extensive knowledge and experience in developing software to interface with custom hardware
  • Proficient with tools for software debugging and troubleshooting (GDB, etc.)
  • Proficient with tools for software performance analysis and optimization
  • Proficient with source control management repositories (such as GIT, SVN, etc.) and CM practices
  • Extensive experience writing high quality unit tests against mock objects
  • Good understanding of object-oriented analysis and design
  • Demonstrated success in collaborating in a fast-paced team environment and delivering high-quality software products using established agile development methodologies (such as Scrum, Kanban, etc.) against formal schedules


  • Possess proven troubleshooting skills
  • Be curious, detail oriented, and analytical, with a proven ability to learn quickly
  • Be customer-focused, team-oriented, and motivated, taking ownership of assigned tasks
  • Have proven ability to self-manage, as well as manage interdisciplinary relationships
  • Have proven verbal and written communication skills

Listed responsibilities are an essential, but not exhaustive list, of the usual duties associated with the position. Changes to individual responsibilities may occur due to business needs.

Concerns regarding COVID-19 continue as positive cases are experienced in the communities in which we operate. Please be aware that, as a condition of employment, Illumina requires proof of COVID vaccination for all U.S.-based employees (subject to limited exceptions) beginning November 1, 2021.

At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and 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 demonstrate our collective commitment to diversity and inclusion in the communities we live and work. 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 require accommodation to complete the application or interview process, please contact To learn more, visit:

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