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

✔️ Base salary — $100,000 annual salary.

✔️ Benefits — comprehensive health, dental, and vision insurance.

✔️ Retirement — 401(k) plan with 6% employer match.