Senior Bioinformatics Pipeline Engineer in Alameda, CA at Quest Diagnostics

Date Posted: 1/6/2020

Job Snapshot

Job Description

Look for more than answers.


At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people.

As a Bioinformatics Pipeline Engineer you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing.

This is a virtual/remote position. The ideal candidate will be located in the greater San Francisco Bay area and will have the ability to travel to meetings ~1x/month.

Senior Bioinformatics Pipeline Engineer - the role

The Bioinformatics Pipeline Engineer will contribute to the development of industry-leading clinical diagnostics services.

You will join a team of bioinformatics scientists, database developers and software engineers whose mission is to automate and deploy robust, high performance clinical analysis pipelines that can accurately and reliably analyze large volumes of data coming primarily from next generation sequencing instrumentation, automate data and reporting workflows, and provide reporting tools to health care practitioners and laboratory scientists.

Job responsibilities:


  • Responsible for macro scale architecture of software technology, including NGS analysis pipeline technology
  • Provide guidance and oversight to multiple development teams working in a regulated environment on different products or technologies to ensure that the technologies interoperate or connect to each other appropriately
  • Participate in the full software development life cycle involving design, implementation, testing, and launching
  • Own the delivery of an entire system or application, and serve as a technical lead on complex projects
  • Consult on process and technology improvements within R&D, Operations, and IT departments
  • Participate in the resolution of operations support requests where NGS analysis pipelines are involved

To qualify, the ideal candidate will have the following skills and experience:


  • BS/MS/PhD in Computer Science, Math, Physics, Bioinformatics or comparable accredited technical degree with 7 or more years of professional experience in software development
  • Proficient in multiple modern programming languages including Python, Perl and shell scripting
  • Experience with Software Development Best Practices
  • Experience with developing containerized pipelines for genomic data analysis
  • Experience with software development and deployment on-premise and at least with one major cloud provider
  • Solid understanding of bioinformatics related to DNA sequencing, including use of standard tools such as BWA, GATK, SAMTools
  • Knowledge of Oracle, SQL and NoSQL databases is nice to have
  • Proven ability to make high-level design choices and developing technical standards, including software coding standards, tools, and platforms in a regulated production environment
  • Familiar with version control systems, preferably Gitlab
  • Ability to handle multiple competing priorities in a fast-paced environment.
  • Experience working within a cross-functional team of scientists, architects, software and database engineers
  • Excellent verbal and written communication skills 

Apply Today


Join us for competitive benefits and development opportunities in a progressive and supportive environment. Help us improve our service, and the experiences of our patients and colleagues. Work with us and together we can be better.

Your Quest career. Seek it out.





All requirements are subject to possible modifications to reasonably accommodate individuals with disabilities. Quest Diagnostics is an Equal Opportunity Employer: Women / Minorities / Veterans / Disabled / Sexual Orientation / Gender Identity.

If you’re interested in career opportunities, but not ready to apply, join our talent network to stay connected to us and receive updates on the latest job opportunities and company news.

Group of people