Job Details

Bioinformatics Scientist

South San Francisco (Hybrid)

Our client is a high-growth genomics company building one of the fastest DNA and RNA sequencing platforms in the world, used daily by thousands of scientists across industry and academia. They are bootstrapped, profitable, and rapidly scaling a global sequencing infrastructure that turns biological samples into answers in hours instead of weeks.

About the Role

This role sits on the core bioinformatics team building the production pipelines and algorithms that power large-scale sequencing services across plasmid, microbial, and RNA-seq applications. You will design, implement, and own high-throughput workflows that process thousands of samples per day while translating noisy real-world sequencing data into accurate, actionable insights for researchers.

Responsibilities

• Design, build, and maintain production-grade bioinformatics workflows that scale to thousands of samples per day using modern workflow orchestration tools.
• Develop and optimize algorithms for microbial genomics, variant calling, and/or bulk and single-cell RNA-seq, from raw reads through to interpretable results.
• Integrate and evaluate cutting-edge sequencing tools and methods, incorporating them into robust, automated pipelines for Illumina and Oxford Nanopore platforms.
• Debug and harden pipelines against real-world data issues, including biological artifacts, platform-specific quirks, and large, heterogeneous datasets.
• Collaborate with product and engineering teams to turn bioinformatics outputs into fast, intuitive user experiences for scientists.
• Mentor teammates, contribute to code review and technical design, and help raise the overall bar on bioinformatics best practices.
• Contribute to the design and implementation of new analyses and services as the company expands beyond plasmid sequencing into broader genomics offerings.

Qualifications

• PhD in Bioinformatics, Computational Biology, Computer Science, Statistics, Biology, or a related quantitative field.
• 3+ years of experience (including post-PhD) developing production bioinformatics pipelines, with at least 2 years in an industry setting.
• Deep expertise in one or more areas: microbial genomics (assembly/metagenomics), large-scale variant calling, or bulk/single-cell RNA-seq analysis.
• Significant hands-on experience with Nextflow (preferred) and/or Snakemake for workflow development and orchestration.
• Proficiency in Python and common bioinformatics tooling, including containerization (Docker/Apptainer or similar), Git, and Linux-based environments.
• Practical experience working with Illumina and/or Oxford Nanopore sequencing data at scale.
• Demonstrated track record of contributing to bioinformatics products or tools beyond one-off analyses or academic pipelines.
• Comfort operating in a fast-moving, high-ownership environment with loosely defined paths and significant autonomy.

Required Skills

• Novel bioinformatics tool or algorithm contributions (e.g., open-source projects, widely used internal tools, or published methods).
• Background in microbial ecology, metagenomics, or related fields that strengthens the team's expertise in microbial genomics.
• Experience building scalable bioinformatics products used by external customers or large internal user bases.
• Prior experience in high-growth startups or similarly dynamic, less structured environments.
• Familiarity with C++ or other performant languages for optimizing core algorithms.