Bioinformatics Pipeline Engineer / South San Francisco

Plasmidsaurus is on a mission to accelerate new cures and promote a healthier planet by unlocking new productivity levels in scientists using DNA tools to bring their ideas to life. The company’s DNA sequencing services are used daily by thousands of innovators, including Nobel Prize winners, dynamic biotech startups, pharmaceutical companies, research labs, and DIY biohackers, and have been cited in more than 800 publications to date. Plasmidsaurus’s global network of labs operates day and night to enable world-changing discoveries.

Job Summary

As a Bioinformatics Pipeline Engineer, you will be responsible for the design, development, and maintenance of bioinformatics pipelines, primarily using Oxford Nanopore reads.

You will collaborate with the bioinformatic and wet lab scientists to understand and implement the specific pipeline goals, while applying your software engineering expertise. A primary focus will be ensuring that our pipelines are robust, scalable, and meet high coding standards. In this job you will:

• Develop and maintain bioinformatics pipelines using Snakemake
• Optimize existing pipelines for performance, reliability, scalability, and maintainability using best practices
• Troubleshoot and resolve issues in pipelines, including handling edge cases related to biological and sequencing artifacts
• Collaborate with both scientists and engineers
• Provide support and training to the tech support team on pipeline usage and troubleshooting
• Explore and integrate new bioinformatics tools and technologies to improve pipelines

Qualifications

• Education and Experience: PhD +1 year production bioinformatics pipeline experience, or Master’s +3 years experience, or Bachelor's +5 years experience
• Required Qualifications:
• Significant Snakemake experience (or Nextflow)
• Production bioinformatics pipeline creation, following best practices
• Conda
• Docker / Apptainer / Singularity
• Git + GitHub
• Python
• Bash
• Ability to write clean, maintainable, and production-ready code
• Strong understanding of molecular biology and sequencing technologies
• Preferred Qualifications:
• Experience with long reads (Oxford Nanopore preferred)
• Performance compiled language (C++, Rust, etc)
• AWS lambda
• AWS S3
• AWS RDS
• Github Actions
• REST API
• Ansible
• SQL alchemy
• GMP software experience

Benefits

• Employee Stock Options
• Health, Dental, and Vision Insurance
• 401(k) with Matching
• Plus: Life Insurance, Mental Health Coverage, Health Advocate, and Gym Membership

Why Plasmidsaurus?

• IMPACT: Your work will directly contribute to accelerating biotech research. This research is one of humanity’s most powerful tools for stopping climate change and developing novel therapies.
• INNOVATION: Work on the cutting edge of biotech and software, introducing indispensable tools to top-tier researchers.
• COMMUNITY: Join a passionate, scrappy team that values close, interactive relationships with our customers and each other.