Senior Automation Engineer

About Clear Labs

Clear Labs builds an end-to-end, FDA-cleared next-generation sequencing (NGS) diagnostics platform. Our system, Clear Dx, combines automated sample-to-report workflows with an assay menu spanning oncology and infectious disease testing. We're a hands-on team building hardware, software, and wet-lab science together, and we're looking for senior engineers ready to take full ownership of systems, not just advise from the sidelines.

Position Summary

We're hiring a Senior Automation Engineer to strengthen the performance, reliability, and validation of the laboratory automation supporting our FDA-cleared NGS diagnostics platform. This is a hands-on, senior role, you'll be at the deck daily, developing methods, troubleshooting hardware, and contributing to formal validation studies alongside our existing automation team.

Location: San Carlos, CA

Travel: No travel required.

Primary Responsibilities

• Contribute hands-on reliability engineering, method development, and troubleshooting expertise for our Hamilton STAR/STAR2 liquid-handling automation fleet running NGS library preparation workflows.
• Help design and execute formal automated-vs-manual equivalence and validation studies for NGS sample prep, in support of regulatory requirements.
• Support root-cause investigation for automation performance issues affecting NGS library quality and sequencing output, working through mechanical, calibration, and liquid-class variables systematically, and flagging labware-related findings to Systems Integration for formal qualification.
• Partner with Regulatory and Quality on validation protocols and documentation for a regulated, FDA-cleared diagnostics workflow.
• Collaborate on vendor and equipment relationships as needed to support fleet performance.

• 8+ years of hands-on experience programming and developing methods on Hamilton STAR/STAR2 (or directly equivalent) liquid handling platforms, including VENUS software, deck layout design, and liquid class development.
• Hands-on troubleshooting of Hamilton hardware and peripherals, e.g., pipetting channels, iSWAP/gripper mechanisms, heater-shakers, plate sealers, and third-party integrated modules.
• Experience maintaining and validating a multi-unit automation fleet, including qualifying individual instruments rather than relying on representative sampling.
• Ability to independently script and modify automated methods in a regulated environment, with full change-control documentation.
• Statistical fluency sufficient to independently evaluate automated performance against validation acceptance criteria.
• A genuine preference for hands-on bench and deck work—this is not a delegate-only role.

Nice to Have

• Working knowledge of NGS library preparation workflows (e.g., hybrid capture and/or amplicon-based enrichment) as executed on automated liquid handling.
• Understanding of how automation method parameters (liquid class, tip type, mixing, incubation) affect NGS library yield, uniformity, and sequencing QC metrics.
• Experience troubleshooting automation-driven failures that manifest downstream in sequencing data (e.g., low on-target rate, coverage dropout, well-position-specific effects).
• Prior oncology diagnostics experience (NGS-based companion diagnostics or comprehensive genomic profiling workflows).

• Salary range: $132,716 to $187,364
• Medical, dental, and vision insurance
• Employer-Sponsored Basic Life/AD&D, Long Term Disability
• Employee Assistance Program (EAP)
• Discretionary Time Off
• Stock Option Plan
• Lunch stipend for days at headquarters

Notice of E-Verify Participation: Clear Labs participates in the federal E-Verify program to confirm the identity and employment eligibility of all newly hired employees. For more information, please review the E-Verify Participation Poster (English/Spanish) and the Right to Work Poster (English/Spanish).

Disclaimer: The above job description is intended to describe the general nature and level of work being performed by individuals assigned to this position. It is not intended to be an exhaustive list of all duties, responsibilities, and skills required. Responsibilities and duties may change or be adjusted to meet the needs of the company, and additional duties may be assigned as necessary. The job description is subject to change at any time at the discretion of the Company.