Lead Bioinformatician/Engineer (Pipelines and Infrastructure)

About the role

Natera is seeking a Lead Bioinformatics Engineer to own pipeline and infrastructure engineering for a research informatics team working on cell-free DNA (cfDNA) screening in Women's and Organ Health. This is an individual contributor role focused on WDL workflows, transitioning toward Nextflow, AWS infrastructure, and associated tooling. You will inherit a working system from the person who built it, with their ongoing support. The role aims to enable scientists to process their own samples end-to-end without engineering intervention.

Responsibilities

• Workflow and Pipeline Engineering: Maintain and improve WDL workflows on AWS Batch and AWS HealthOmics. Own the integration of new Nextflow workflows and existing WDL workflows on unified tooling and infrastructure. Simplify pipelines to allow scientists to run them correctly without engineering support.
• Infrastructure and Operability: Own the team's AWS infrastructure, managed as code in Terraform. Enhance reliability, reproducibility, and observability across compute environments. Build testing, monitoring, and alerting to surface failures before scientists encounter them.
• Tooling and Developer Productivity: Develop and harden internal tooling to reduce manual work, including support for triaging production issues. Streamline testing, documentation, and handoff of new capabilities.
• Ways of Working: Use coding agents as a routine part of engineering for implementation, code review, investigation, and operational triage. Maintain ownership of shipped work, reviewing and testing agent-written code to the same standard as your own. Help the team evaluate and adopt these tools.
• Collaboration and Handoff: Partner with science leads and data scientists to bring new methods into production pipelines and provide first-line review of their changes. Work with the production organization to ensure readiness for capabilities transitioning out of research.

What Success Looks Like After a Year

• You own the team's pipelines and infrastructure without supervision.
• Transition to new workflows on the same tooling and infrastructure from existing workflows is complete.
• Scientists run and debug their own pipeline work without requiring your intervention first.
• Operational interruptions to the team's scientific work are reduced.
• Agent-assisted work is a normalized part of your workflow.

Requirements

• Degree in Bioinformatics, Computer Science, Computational Biology, or a related field. Equivalent professional experience is fully accepted.
• 4+ years of software or pipeline engineering experience, preferably in life sciences, sequencing, or production-adjacent settings. Relevant experience is counted from the point your work became substantially independent.
• Demonstrated end-to-end ownership of a system in production, not just initial development.

Skills

• Strong Python and software engineering fundamentals, including testing and debugging.
• Experience with at least one workflow system: Snakemake, CWL, WDL, Nextflow, or similar.
• Real cloud experience, ideally AWS, including managing infrastructure as code (Terraform preferred).
• Solid Linux, container, and version control practices.
• Experience building and maintaining at least one AI-assisted workflow, with clear understanding of its impact and reliability.
• Proven ability to quickly learn unfamiliar tools, beyond specific tools listed on your resume.
• Clear written communication, including actionable documentation.
• Strong candidates may also have:
  • Direct WDL or Nextflow experience.
  • Familiarity with AWS Batch or HealthOmics.
  • Scientific curiosity to understand the biology behind pipelines and ask insightful questions.

Pay

Remote USA: $130,900—$163,600 USD. Actual compensation is based on factors unique to each candidate, including skill set, experience, certifications, and location.

Benefits

• Comprehensive medical, dental, vision, life, and disability plans for eligible employees and dependents.
• Free testing for Natera employees and their immediate families, plus fertility care benefits.
• Pregnancy and baby bonding leave.
• 401k benefits.
• Commuter benefits.
• Generous employee referral program.