Architect, develop, and maintain scalable, production-ready bioinformatics pipelines for next-generation sequencing data, with primary ownership of workflows implemented in Nextflow and WDL
Lead pipeline design decisions with a strong emphasis on modularity, reusability, robustness, scalability, and maintainability
Refactor and optimize existing pipelines to improve performance, cost efficiency, fault tolerance, and ease of extension
Establish and enforce best practices for workflow development, including parameterization, versioning, provenance tracking, and reproducibility
Design and implement comprehensive testing strategies for pipelines and supporting code, including unit, integration, and end-to-end tests
Deeply understand and troubleshoot complex sequencing data processing pipelines across multiple stages (QC, alignment, methylation calling, feature generation, etc.)
Partner closely with Research, Machine Learning, and Platform Engineering teams to transition research workflows into production-grade systems
Support training and evaluation of machine learning models by enabling efficient data generation and large-scale distributed execution on AWS
Participate in and lead code reviews and design reviews, mentoring other engineers and scientists on workflow and software engineering best practices
Contribute to pipeline documentation, onboarding materials, and internal standards.

Requirements

MS or PhD in Computer Science, Bioinformatics, Computational Biology, or a related field, with a strong focus on cancer genomics or epigenomics
Extensive hands-on experience developing bioinformatics pipelines using Nextflow and/or WDL, including complex multi-step NGS workflows
Proven track record of building and supporting production-level bioinformatics software in regulated or high-reliability environments
Deep understanding of software engineering best practices, including workflow design patterns, testing, version control, CI/CD, code review, and documentation
Strong experience with containerized workflows (Docker) and execution on cloud platforms; AWS experience strongly preferred
Expertise in distributed and parallel computing, including workflow execution engines and cloud-native scaling strategies
Experience profiling and optimizing pipelines and code for runtime, memory usage, and cost efficiency
Strong understanding of sequencing technologies and data types, particularly methylation and epigenomic assays
Advanced programming skills in Python, including experience with scientific and data-processing libraries (e.g., Pandas, NumPy, scikit-learn)
Expert-level proficiency with Linux, shell scripting, and command-line bioinformatics tools
Ability to work independently, lead technical initiatives, and manage multiple priorities in a fast-paced environment
Strong communication skills and a collaborative mindset.

Benefits

Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits. Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program!

Applicant Tracking System Keywords

Tip: use these terms in your resume and cover letter to boost ATS matches.

Hard Skills & Tools

bioinformatics pipelinesNextflowWDLPythonDockerAWSdistributed computingparallel computingdata processingsoftware engineering best practices

Soft Skills

leadershipcommunicationcollaborationindependencementoringtechnical initiative managementprioritizationproblem-solvingdocumentationtraining