Senior/Lead Bioinformatics Engineer

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