Bioinformatics Data Engineer III

Job ID
Regular Full-Time
Fred Hutchinson Cancer Research Center
Information Technology


Fred Hutchinson Cancer Center is an independent, nonprofit, unified adult cancer care and research center that is clinically integrated with UW Medicine, a world leader in clinical care, research and learning. The first National Cancer Institute-designated cancer center in the Pacific Northwest, Fred Hutch’s global leadership in bone marrow transplantation, HIV/AIDS prevention, immunotherapy, and COVID-19 vaccines has confirmed our reputation as one of the world’s leading cancer, infectious disease and biomedical research centers. Based in Seattle, Fred Hutch operates eight clinical care sites that provide medical oncology, infusion, radiation, proton therapy, and related services, and network affiliations with hospitals in five states. Together, our fully integrated research and clinical care teams seek to discover new cures to the world’s deadliest diseases and make life beyond cancer a reality.


At Fred Hutch, we believe that the innovation, collaboration, and rigor that result from diversity and inclusion are critical to our mission of eliminating cancer and related diseases. We seek employees who bring different and innovative ways of seeing the world and solving problems. Fred Hutch is in pursuit of becoming an antiracist organization.  We are committed to ensuring that all candidates hired share our commitment to diversity, antiracism, and inclusion.   


Job Summary:

The Data Engineer III designs and builds automated computational workflows for the analysis of large-scale datasets which serve the needs of researchers at Fred Hutch and affiliated institutions. Using their scientific experience in the analysis of “-omics” datasets and knowledge of the UNIX command line and common bioinformatics tools, they will work collaboratively to contribute best-in-class analysis tools to the Data Portal resources offered by the Data Core.


Scope of Responsibilities:

The Data Engineer III reports to the Associate Director of the Data Core and will be responsible for developing best-in-class bioinformatics workflows which will be integrated with a larger data platform for the manipulation, management, and delivery of data produced by high-throughput instrumentation in Shared Resources.


The Data Engineer III will be responsible for validating the accuracy of overall workflows using scientifically appropriate test datasets and communicating their utility to a larger team of data engineers and software developers. Based on user feedback, they will be responsible for troubleshooting any errors which are identified and implementing any corrective actions which may be needed. As part of this overall effort, they will be responsible for building, organizing, and maintaining additional data resources including Docker images, component process configurations, reference databases, and documentation.

The workflows developed by the Data Engineer III will be used by a community of researchers who have submitted physical specimens for analysis by Shared Resources, including genomics, proteomics, microscopy, etc. The Data Engineer will help support the team’s efforts to communicate the use and interpretation of analysis results to this community of researchers, who may not have a technical background in bioinformatics analysis.


  • Researching, developing, and testing the most appropriate bioinformatics approach for the analysis of high-dimensional ‘omics’ datasets (primarily genomics, but also encompassing proteomics, high-throughput microscopy, metagenomics, etc.), adopting public workflows when appropriate and developing novel workflows when necessary. (60%)
  • Contributing domain expertise to the scientific requirements used to guide the development of analysis tools for lab-based end-users, including the technical documentation needed to describe workflow execution to a non-scientific audience. (10%)
  • Collecting, documenting, and maintaining reference databases used by analytical workflows, such as compressed alignment indices, k-mer databases, and gene annotation models. (10%)
  • Reviewing scientific literature and staying up-to-date on the latest developments in bioinformatics analysis as relevant to the end-users of Shared Resources instrumentation and services. (10%)
  • Working to develop and deliver documentation materials used to educate end-users on the proper use of specific analysis workflows, as well as the meaningful interpretation of the associated results. (10%)



  • Master's with 4 years of related experience or PhD required
  • Command-line interface (BASH);
  • UNIX-based file systems (Linux or OSX);
  • Data manipulation using R or Python 3;
  • Installing and using genomics command-line utilities (e.g. BWA, Samtools);
  • Experience processing high-throughput genome sequencing datasets (e.g. Illumina, PacBio);
  • Strong organizational skills, including the ability to work independently



  • 6 years of related experience
  • Experience using workflow manager tools (e.g. Nextflow, Cromwell, Snakemake);
  • Experience using batch computing systems (e.g. SLURM, PBS, AWS, Google Cloud);
  • Proficiency with R/Bioconductor or Python/Pandas/Scipy
  • Public speaking to technical and non-technical audiences;
  • Software version control (git).


Fred Hutch has a mandatory COVID-19 vaccine requirement, with exceptions only for approved medical or religious accommodations.
As a condition of employment, newly hired employees must provide proof of vaccination or initiate the accommodations process before their first day of employment. 


A statement describing your commitment and contributions toward greater diversity, equity, inclusion, and antiracism in your career or that will be made through your work at Fred Hutch is requested of all finalists.

Our Commitment to Diversity

We are proud to be an Equal Employment Opportunity (EEO) and Vietnam Era Veterans Readjustment Assistance Act (VEVRAA) Employer. We are committed to cultivating a workplace in which diverse perspectives and experiences are welcomed and respected. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability (physical or mental), marital or veteran status, genetic information, sexual orientation, gender identity, political ideology, or membership in any other legally protected class. We are an Affirmative Action employer. We encourage individuals with diverse backgrounds to apply and desire priority referrals of protected veterans. If due to a disability you need assistance/and or a reasonable accommodation during the application or recruiting process, please send a request to our Employee Services Center at or by calling 206-667-4700.


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