Bioinformatics Scientist 1 - 7226BR

Illumina, Inc.
Job Location
San Diego, CA 92121
Job Description

Do you want to make a difference? Illumina’s mission is to improve human health by unlocking the power of the genome. If that inspires you, let’s talk. We’ve built a culture fueled by innovation, collaboration and openness, and established ourselves as the global leader in DNA sequencing and array-based technologies. Our people and our technology change lives by driving advancements in life sciences, oncology, reproductive health, agriculture and other emerging markets. Life at Illumina is about working with teammates who are deeply passionate about what we do, because we know that our work has the power to improve lives. We’re an established company with a track record of phenomenal growth. Just check out our investor events and presentations to learn about our financial accomplishments. Our growth isn’t just in financials, we’ve been busy hiring the best and the brightest. Perhaps that’s why MIT has ranked Illumina near the top of its World’s Smartest Companies each of the last three years. If you thrive in a brilliant, fast-paced, and mission-driven environment, Illumina is the place for you. Join the journey of a lifetime. Join Illumina.

Bioinformatics Scientist
Our team specializes in developing tools and workflows to analyze somatic mutations found in tumor and normal tissue samples. One of the many challenges in this area involve analyzing archived FFPE samples that often present problematic sequence artifacts. We devise methods to counteract these sources of error and to continually expand the limits of detection for our tools.
Our team is actively developing variant annotation tools that are both more accurate than existing tools, but also orders of magnitude faster. We aspire to bridge the gap between variant discovery and providing actionable information for research and clinical use.
We are seeking an exceptional individual to join our team in developing analysis tools that will be used by researchers and clinicians worldwide. These tools will be incorporated in Illumina’s expanding oncology portfolio and used in high visibility projects such as the 100,000 Genomes Project.

  • Creation of novel sequence analysis workflows (i.e. read alignment, variant calling, and variant annotation) to support both research and clinical products.
  • Design, prototype, and implement computational algorithms that utilize both statistical and machine learning approaches.
  • Software optimization at the design, algorithm, and source code level.
  • Identify opportunities to improve the bioinformatics user experience and implement solutions.
  • Collaborate with internal project teams and with external organizations.
  • Contribute to the bioinformatics open source community.


  • Strong background in developing software with multiple languages and multiple platforms. Experience with C#, C++, Java, and Go is highly advantageous.
  • Personal initiative and ability to work effectively as part of a team.
  • Familiarity with applying statistical approaches to algorithm development.
  • Superior written and verbal communication skills.
  • Basic knowledge of genomics, genetics, and sequencing technologies.


  • Familiarity with agile software development processes (e.g. scrum).
  • Hands-on experience with sequence analysis tools such as samtools and GATK.
  • Experience with sequencing data analysis.
  • Experience with cloud computing, parallel computing, and big data.
  • Familiarity with genomic annotation databases (e.g. RefSeq, Ensembl, dbSNP, DGV, dbVAR, ClinVar, COSMIC, and ExAC).
  • Experience with using version control systems such as git and TFS.


  • Master’s degree or PhD in bioinformatics, biology, engineering, physical sciences, computer science, mathematics, statistics, or equivalent.

When you join the high-performing team at Illumina, your work takes on new meaning. Our growth, our positive culture, and the impact our products are having in the world ignite a passion that drives our people forward. And together, we accomplish beyond expectations.




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 858-246-8959. To learn more, visit:

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