Bioinformatics Production Engineer

Natera; South San Francisco (CA); On-site; USD 114,000 - 143,000; Full time

Benefits offered by this job

Long-term equity awards

401(k) with company match

Generous paid time off

Job summary

Natera in California is seeking a data analyst to support product development, validation studies, and incoming experiment analyses. You will analyze sequencing data, improve the data processing pipeline, and troubleshoot data quality and system integration issues.

The role emphasizes cross-functional collaboration with biology, software, and lab operations teams, plus producing formal study plans and technical reports. HIPAA/PHI privacy training is required within 30 days of hire.

Qualifications

• Knowledge of biological concepts related to molecular biology, cell biology, and genetics.
• Experience with sequencing assays and genomics analyses.
• Ability to produce technical documentation for validation reports.

Responsibilities

• Analyze high-throughput DNA sequencing data to support product development and validation studies.
• Improve data processing pipelines and production workflows.
• Troubleshoot data quality, pipelines, and system integration.
• Collaborate cross-functionally with biology, software engineering, and operations teams.
• Produce high-quality written technical reports and study plans.
• Adhere to PHI privacy and security policies; complete required compliance training.
• Stay current with HIPAA/PHI privacy and General Policies and Procedures.

Skills

Genomics knowledge

NGS data analysis

Python for data analysis

Linux command line

SQL databases

Pipeline/workflows (WDL/Nextflow)

Written documentation

LLMs for workflow optimization

Education

Bachelor's degree in Biomedical Engineering, Computer Science, Bioinformatics, or related equivalent field

Master’s degree in a relevant scientific or technical discipline

Tools

Nextflow

WDL

Plotly

Job description

PRIMARY RESPONSIBILITIES

• Data Analysis & Processing: Analyze high-throughput DNA sequencing data and perform basic data analysis to support product development, validation studies, and incoming experiment analysis requests.
• Pipeline Improvement & Support: Help move data through the analysis pipeline while proactively identifying and implementing improvements to production workflows.
• Troubleshooting: Investigate and resolve technical issues related to data quality, analysis pipelines, and system integration.
• Cross-Functional Collaboration: Communicate effectively and work collaboratively with cross-functional teams, including biology, software engineering, lab operations, and medical/legal affairs.
• Documentation: Produce high-quality written documentation, including formal study plans and technical reports.
• Compliance & PHI Safety: Regularly handle Protected Health Information (PHI) in both paper and electronic formats, ensuring strict adherence to data privacy technologies and protocols.
• Training & Certification: Complete required HIPAA/PHI privacy, security, and General Policies and Procedures Compliance training within the first 30 days of hire, and maintain current status on all ongoing company training requirements.

QUALIFICATIONS

Minimum Qualifications

• Bachelor’s degree in Biomedical Engineering, Computer Science, Bioinformatics, or a related equivalent field.
• 2+ years of relevant professional experience.

Preferred Qualifications

• Master’s degree in a relevant scientific or technical discipline.
• Previous professional experience within the biotechnology, diagnostics, or pharmaceutical industry.

KNOWLEDGE, SKILLS, AND ABILITIES

• Knowledge of biological concepts related to molecular biology, cell biology (specifically related to DNA/RNA), and genetics.
• Experience and knowledge of how Sequencing Assays work.
• Experience using Python for data analysis and plotting is preferred.
• Experience using Linux command-line tools and relational databases (SQL) preferred, knowledge of data visualization tools/platforms a plus (plotly).
• Knowledge of genomics, relevant NGS analyses (mapping, variant calling, etc.), and NGS file types is required. e.g. Know how to run pipelines and knowledge of pipeline platforms/languages (WDL, Nextflow).
• Ability to produce high quality written documentation for varying audiences, e.g. validation reports
• Familiarity with Large Language Models (LLMs), such as Claude Code, and how to leverage them to streamline workflows and tasks.
• Ability to work independently while managing multiple objectives and timelines.
• Desire to work in a fast-paced environment with potential for high impact in a small team.
• Team player, self-motivated, and detail-oriented.

Compensation & Total Rewards

This range reflects a good-faith estimate of the base pay we reasonablyexpect 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:

• Long-term equity awards
• 401(k) with company match
• Generous paid time off and company holidays
• Additional wellness and work-life benefits

Compensation Range

$114,400 - $143,000 USD

OUR OPPORTUNITY

Natera™ 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.

WHAT WE OFFER

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.

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