Senior​/Lead Bioinformatics Engineer San Carlos, CA

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.

• 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.

• 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, Num Py, 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.

Compensation range: $144,000 – $180,000 USD. Position eligible for additional compensation and benefits through Natera’s robust Total Rewards program, including annual performance incentive bonus, long‑term equity awards, 401(k) with company match, generous paid time off and company holidays, and additional wellness and work‑life benefits.

• Annual performance incentive bonus
• Long‑term equity awards
• 401(k) with company match
• Generous paid time off and company holidays
• Additional wellness and work‑life benefits

Natera is proud to be an Equal…