Senior/Lead Bioinformatics Engineer
About The Position
Natera is seeking a Senior/Lead Bioinformatics Engineer to join the Bioinformatics Research team focused on Epigenomics in Oncology. Natera’s mission is to transform disease management worldwide by leveraging information from a simple blood draw to enable early detection and guide treatment decisions. This role will provide technical leadership in the design, development, and maintenance of large-scale, production-grade bioinformatics pipelines, with a strong emphasis on workflow orchestration using Nextflow and WDL. The ideal candidate brings deep hands-on experience building, optimizing, and operating NGS pipelines in cloud environments, and is comfortable bridging research and production engineering.
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
Responsibilities
- 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
Benefits
- Comprehensive health benefits (medical, dental, vision)
- 401(k) with company match
- Generous paid time off and company holidays
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What This Job Offers
Job Type
Full-time
Career Level
Mid Level
