Natera is seeking a Senior Bioinformatics Scientist to lead the architecture, development, and automation of high-throughput genomic pipelines. This role is responsible for building production-grade software tools to analyze next-generation sequencing (NGS) data including variant calling, fusion detection, and data quality control. The ideal candidate combines a deep understanding of sequence alignment algorithms with strong object-oriented programming skills to design scalable computational workflows in a fast-paced, mission-driven environment.

Primary Responsibilities:

• Analyze complex genomic datasets leveraging scaled in-house pipelines, partnering cross-functionally with wet-lab scientists and statisticians to rapidly deliver data-driven answers to critical research goals.
• Architect, build, and deploy automated analysis pipelines for diagnostic tests, integrating robust capabilities for fusion detection, variant calling, and automated quality control metrics.
• Engineer novel genomic analysis tools and proactively identify optimization pathways to enhance pipeline accuracy and efficiency.
• Participate in code reviews, technical documentation, and the continuous improvement of core computational workflows.
• Coordinate directly with downstream infrastructure teams to ensure R&D tools scale efficiently into production systems.

Qualifications:

• Ph.D. in Bioinformatics, Computer Science, Engineering, Biochemistry, or a related quantitative field with 0-3 years of professional experience
• Masters in Bioinformatics, Computer Science, Engineering, Biochemistry, or a related quantitative field with 4-6 years of professional experience 

Knowledge, Skills, and Abilities:

• Deep theoretical and practical understanding of high-throughput DNA sequence data analysis, including mapping, sequence alignment, and variant calling workflows.
• Advanced understanding of data structures, algorithm design, and computational complexity.
• Strong Python programming skills, including fluency with the scientific computing stack (NumPy, Pandas, Scikit-learn) for data manipulation, analysis, and automation.
• Proficiency with workflow languages — Nextflow or WDL strongly preferred — for developing, versioning, and deploying scalable bioinformatics pipelines.
• Extensive experience in distributed computing and cloud environments; AWS strongly preferred, with hands-on use of cloud-native tools such as AWS Batch, S3, or Lambda.
• Deep expertise navigating Linux environments, utilizing command-line tools, and writing efficient shell scripts.
• Demonstrated technical autonomy and rigorous data discipline when troubleshooting high-complexity algorithmic challenges.
• Excellent communication skills with a proven track record of explaining computational results clearly to cross-functional stakeholders.
• Prior experience working with relational databases, particularly MySQL, is highly desirable.