Research Associate, NGS Pipeline Operations

About the Role

Taxa engineers the microbiome. We design live bacterial therapeutics and deliver them to people. Sequencing is the backbone of that work: every strain we ship, and sample we get back, passes through our NGS pipeline. This role owns the day-to-day operation of that pipeline and keeps it running at throughput. We are seeking a reliable, experienced pipeline operator to run and improve our core NGS workflows end to end. This is fundamentally a next-generation sequencing role: library prep, whole-genome and metagenomics sequencing across short- and long-read platforms, executed as dependable production operations rather than one-off experiments.

Key Responsibilities

• Operate and maintain liquid-handling and sample-handling systems.
• Navigate the practical realities of automation (plate and tube formats, racking, sample tracking, instrument integration).
• Harden unit operations.
• Interrogate every reagent, kit, instrument, and QC step a sample touches.
• Run workflows that are reproducible, traceable, and dependent on processes rather than people.
• Operate as an independent scientist within a lean, highly skilled team, with full ownership over workflows, research agenda, and results.

Requirements & Tech Stack

• NGS pipeline operations: Hands-on, high-throughput expertise across the sequencing workflow: NGS library prep, isolate whole-genome sequencing, and shotgun metagenomics on short- and long-read platforms (Illumina, ONT, Element).
• Run sequencing as production, with the QC discipline to keep data quality high at volume.
• Laboratory automation expertise: Deep experience using and managing a diverse array of laboratory automation equipment.
• Develop and run high-throughput protocols on liquid-handling and sample-handling robots (e.g., Opentrons, Tecan, Avidien/Apricot, QPix).
• Handle hardware integration, deck and labware configuration, and sample-tracking systems.
• Bacterial isolation and culture: Isolating, culturing, and maintaining diverse bacteria at scale, including selective/differential media, colony picking and arraying into plate formats, and cryobanking, including non-model organisms with slow or fastidious growth.
• Laboratory and data organization: Maintains a spotless, efficient lab; tracks every sample, plate, reagent, and instrument with precision; uses ELNs and structured metadata so workflows are fully documented, traceable, and reproducible.
• Full on-site availability – based in or willing to relocate to the Bay Area.
• Flexible working hours – Availability for irregular managing the pipeline at irregular hours: morning, evening, or weekends.
• Authorized to work in the U.S.

Highly Desirable Experience

• Microbial-interaction and phenotypic/genotypic assays: Designing and running in vitro screens across isolates (e.g., growth/inhibition and antagonism assays, colony PCR, marker genotyping, arrayed functional and co-culture assays) and building triage logic that prioritizes which strains advance.
• Miniaturization, cost-down, and method development from literature: Scaling workflows down in volume and cost while holding data quality, and rapidly evaluating, implementing, and adapting protocols from publications to specific platforms.
• Troubleshooting complex failures: Diagnosing multi-factor issues spanning assay chemistry, instrumentation, and sequencing.
• Low-biomass and challenging samples: Recovering and processing organisms from low-biomass, mixed, or otherwise difficult primary samples.

Compensation

• Base salary: $100,000 annual salary.
• Benefits: comprehensive health, dental, and vision insurance.
• Retirement: 401(k) plan with 6% employer match.