Senior/Lead Bioinformatics Engineer

LOCATION: Position is available as a hybrid position in San Carlos, California as well as a remote position within the US.

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.

PRIMARY 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

QUALIFICATIONS:

• MS or PhD in Computer Science, Bioinformatics, Computational Biology, or a related field, with a strong focus on cancer genomics or epigenomics

KNOWLEDGE, SKILLS, AND ABILITIES:

• 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