Senior Bioinformatics Scientist

Senior Bioinformatics ScientistSan Carlos, CANatera 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 experienceMasters in Bioinformatics, Computer Science, Engineering, Biochemistry, or a related quantitative field with 4-6 years of professional experienceKnowledge, 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.Compensation & Total Rewards This range reflects a good-faith estimate of the base pay we reasonably expect to offer at the time of hire. Final compensation will vary based on experience, qualifications, and internal equity considerations. This position is also eligible for additional compensation and benefits through Natera's robust Total Rewards program, including: Annual performance incentive bonus Long-term equity awards Comprehensive health benefits (medical, dental, vision) 401(k) with company match Generous paid time off and company holidays Additional wellness and work-life benefitsCompensation Range$130,700 - $163,400 USDNatera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women's health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other. When you join Natera, you'll work hard and grow quickly. Working alongside the elite of the industry, you'll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management.Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits. Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program!Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws.If you are based in California, we encourage you to read this important information for California residents.