Research Associate, NGS Pipeline Operations

Taxa; San Francisco (CA); On-site; USD 120,000 - 180,000; Full time

Benefits offered by this job

Health insurance

401(k) with employer match

Job summary

Taxa is seeking a Research Associate to own and operate our NGS pipeline in the San Francisco Bay Area. You will manage library prep, whole-genome sequencing, and metagenomics across platforms, ensuring production-level throughput with robust QC. Strong automation experience and hands-on lab work are essential.

You will oversee liquid-handling systems, plate formats, and sample-tracking, delivering reproducible workflows and owning your research agenda and results in a lean, capable team.

Qualifications

• Hands-on, high-throughput NGS pipeline operations including library prep and sequencing.
• Deep experience with lab automation equipment and high-throughput protocols.
• Bacterial isolation, culture, and cryobanking at scale.
• Strong lab organization with traceable, documented workflows.
• Willingness to work on-site in the Bay Area.
• Authorized to work in the U.S. (no visa sponsorship).

Responsibilities

• Operate and maintain the NGS pipeline end-to-end.
• Run and improve core sequencing workflows across platforms.
• Work with automated liquid-handling and sample-handling robots.
• Ensure reproducible, traceable, and well-documented workflows.
• Own your workflows, research agenda, and results.

Skills

NGS pipeline ops

Lab automation

Bacterial isolation

Lab organization

On-site Bay Area

Flexible hours

US work authorization

Tools

Opentrons

Tecan

Avidien/Apricot

QPix

Job description

Research Associate, NGS Pipeline Operations

The Opportunity (Full-time, San Francisco)

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. Much of the pipeline is automated, so deep, hands-on fluency with a diverse array of laboratory automation equipment is central to the job.

You will operate and maintain liquid-handling and sample-handling systems, navigate the practical realities of automation (plate and tube formats, racking, sample tracking, instrument integration), and harden unit operations.

Nothing in your pipeline is a black box: you've interrogated every reagent, kit, instrument, and QC step a sample touches. You run workflows that are reproducible, traceable, and dependent on processes rather than people. You'll operate as an independent scientist within a lean, highly skilled team, with full ownership over your workflows, your research agenda, and their results.

Required Qualifications

• 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). You 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. You work closely with the team to develop and run high-throughput protocols on liquid-handling and sample-handling robots (e.g., Opentrons, Tecan, Avidien/Apricot, QPix). You also handle hardware integration, deck and labware configuration, and sample-tracking systems as part of your core skill set.
• 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. — Visa sponsorship is not available for this role.

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.

Transparent Compensation

• Benefits — comprehensive health, dental, and vision insurance.
• Retirement — 401(k) plan with 6% employer match.