Software Engineer - Pipeline Developer

Company: Mayo Clinic
Location: Rochester
Posted on: January 9, 2026

Job Description:

Mayo Clinic’s tech culture is rooted in passion for technology, embraces innovative thinking and strives for high performance. Our teams drive change in health care through comprehensive connected health and digital transformation strategies. Some examples of our major initiatives are: • Utilizing artificial intelligence and machine learning principles to develop next generation patient centric care systems • Transforming the practice by applying data science techniques to discover new approaches to health care delivery • Leveraging Enterprise Architecture to construct integration centricity, promote data liquidity, and provide innovation support This transformation creates, connects and applies integrated knowledge to deliver the best health care, health guidance and health information to patients, customers, partners, providers, employees anywhere and anytime so the needs of the patient come first. Why Mayo Clinic Mayo Clinic is top-ranked in more specialties than any other care provider according to U.S. News & World Report. As we work together to put the needs of the patient first, we are also dedicated to our employees, investing in competitive compensation and comprehensive benefit plans – to take care of you and your family, now and in the future. And with continuing education and advancement opportunities at every turn, you can build a long, successful career with Mayo Clinic. Benefits Highlights • Medical: Multiple plan options. • Dental: Delta Dental or reimbursement account for flexible coverage. • Vision: Affordable plan with national network. • Pre-Tax Savings: HSA and FSAs for eligible expenses. • Retirement: Competitive retirement package to secure your future. Responsibilities Mayo Clinic Genomics and Emerging Systems Unit is recruiting a Software Engineer for a Next Generation Sequencing Pipeline Development and Validation programmer to provide application development and support for genomic analysis, tooling and infrastructure focused on automating and simplifying the data processes for both externally and internally generated genomics data from inception through final bioinformatics analysis and delivery. This position will support the needs of the Clinical Genome Sequencing Laboratory (CGSL). This position will work closely with our Consultants and our Bioinformatics team along with the Genetic Counselors, Lab Supervisors, Technicians and Operators to align, develop, and solution the tools necessary to implement a wide range of Next Generation Sequencing (NGS) tests from small gene panels to Whole Genome Sequencing, to the Epigenome and Microbiome tests. This position will be responsible for the design, development, implementation, and maintenance of custom system software, and/or the installation and maintenance of purchased systems software, as well as the configuration and support of computational cluster hardware systems in a variety of genomics and bioinformatics areas. Active participation in Agile and DevOps methodologies is expected, utilizing tools such as GitHub, Azure DevOps (ADO), Azure Pipelines, and CI/CD frameworks. Responsibilities may also extend to deployment automation and configuration management using platforms like Terraform and Azure Pipelines, supporting both on-premises and cloud-hosted applications. Evaluates alternative approaches and presents recommendations to teams and unit leadership. Regularly reviews applications and makes modifications and/or updates to ensure currency and functionality within established environment. Produces and maintains documentation such as system requirements, designs, resource inventories, and plans. Provides technical and project leadership to other staff members, demonstrates initiative, and works independently as needed to accomplish responsibilities. Works effectively across departmental organizations gaining consensus of stakeholders. May interface with vendor support service groups or other external support teams to ensure proper escalation during outages or periods of degraded system performance. Acts as a liaison to Mayo departments and vendors to adequately support the division’s computing systems. Interfaces routinely with colleagues who may be located at any of the Mayo Group practices to perform job responsibilities requiring virtual collaboration and partnership. This position will be required to provide 24/7 on-call support in a team rotation. Designs and builds back-end services that support our portfolio of data-centric clinical and analytic applications. These applications leverage cloud computing, big data, mobile, data science, data warehousing, machine learning using state of the art software development applications and frameworks. Our Software Engineers ensures that these cloud-based micro-services adhere to uptime and accuracy targets, are resilient, and scale as data volumes and traffic increase. They work closely with the data engineering, platform, and solutions teams to develop applications as required to benefit our practice and patients. Works closely with the Product Owners, Product Managers, Architects to translate requirements into code. Developing services around data warehousing, big data, cloud computing, business intelligence, analytics and machine learning. Participate in DevOps, Agile, continuous development and integration frameworks. Programming in high-level languages such as Go, Python, Java etc. Work on deployment automation/configuration management with tools including but not limited to ADO, Puppet, Chef or Ansible or Azure Pipelines, CloudFormation, Terraform following a DevOps model. Ensure all appropriate documentation of processes and source code is created and maintained. Communicate effectively with peers, leaders, and customers throughout the organization. Participate in expert level troubleshooting and resolve problems through root cause analysis, data and system investigation. Continues to build knowledge of the organization, processes and customers. Performs a range of mainly straightforward assignments. Uses prescribed guidelines or policies to analyze and resolve problems. Receives a moderate level of guidance and direction. This is a full time, remote position within the United States. Mayo Clinic will not sponsor or transfer visas for this position including F1 OPT STEM. Qualifications • Bachelors Degree in Computer Science/Engineering or related field; Or an Associates’ degree in Computer Science/Engineering or related field with an additional 2 years of experience as described below. • Have working knowledge and experience of Software Engineering with a minimum of internships and a minimum of 1 yr. of experience, or 2yrs of experience coding applications or services in a high-level language (C, C++, Golang, Java, C# etc.). • Demonstrated problem solving and time management skills. • Possesses strong technical aptitude for designing and implementing software solutions. • Experience with modern application development frameworks • Knowledge of professional software engineering practices & best practices for the full software development life cycle, including coding standards, code reviews, source control management, build processes, testing, and operations. • Deep hands-on technical expertise, excellent verbal and written communication skills. • Experience with Agile software development techniques. Preferred qualifications for this position include: • Ability to use a wide variety of open-source technologies and cloud-based services. • Experience with Google and Azure cloud environments • Experience in databases, analytics, big data systems or business intelligence products • Experience with building high-performance, highly available and scalable distributed systems. • Experience developing software for healthcare related industries. Preferred Qualifications: • Demonstrated ability to learn new scripting languages and tools quickly • Knowledge of bioinformatics applications and tools and pipelines such as Illumina BCL Conversion, Genomic Aligners and Variant callers such as GATK or Sentieon. • Knowledge of Nextflow or other pipeline management software a plus. • Knowledge of Python, BASH, R and other scripting and Linux/Unix tools. • Previous knowledge of Genetics software pipelines and tooling for the laboratories • Must possess excellent analytical, problem-solving, and technical design skills. • Must have knowledge of system architecture and design principles, software development methodologies, and computer programming. • Must be willing to work in an Agile team environment as well as being comfortable working independently with minimal supervision • Must be highly motivated and willing to learn and implement leading edge technologies. T • The candidate must be comfortable interacting with researchers and consultants both internal and external to Mayo Clinic. • Experience with clustered/distributed environments using Oracle Grid Engine is highly desirable. • Familiarity with cloud integration CLI tooling such as awscli, gcloud, and azurecli is a plus. • Candidate with genomics domain expertise and some exposure to clinical or research laboratory work and equipment are highly desirable • Bachelors or Masters degree in Computer Science or related field is preferred

Keywords: Mayo Clinic, Rochester , Software Engineer - Pipeline Developer, IT / Software / Systems , Rochester, Minnesota