Senior/Lead Bioinformatics Engineer

Natera is seeking a Senior/Lead Bioinformatics Engineer to join the Bioinformatics Research team focused on Epigenomics in Oncology. This role will provide technical leadership in the design, development, and maintenance of large-scale bioinformatics pipelines, emphasizing workflow orchestration using Nextflow and WDL.

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

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
• AWS experience strongly preferred