Bioinformatics Pipeline Engineer

About Plasmidsaurus

Plasmidsaurus is on a mission to accelerate new cures and promote a healthier planet by unlocking a new level of productivity for scientists who use DNA tools to bring their ideas to life. Our DNA sequencing tools are used daily by thousands of innovators, including Nobel prize winners, dynamic biotech startups, research labs, and DIY biohackers. Our global network of labs operates day and night to enable world-changing discoveries. In 2024, we saved these scientists 2 million hours of time, radically accelerating their research. Every team member at Plasmidsaurus plays a crucial role in driving forward the future of biotech research.

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

QualificationsEducation and Experience

• PhD +3 years of developing production bioinformatics pipelines, or significant relevant work 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

• Experience with Oxford Nanopore and Illumina sequencing

Preferred Qualifications:

• Performance compiled language (C++, Rust, etc)

• AWS lambda

• AWS S3

• AWS RDS

• Github Actions

• REST API

• Ansible

• SQL alchemy

• SQL (PostgreSQL)

Compensation & Benefits

• Employee Stock Options

• 4 Weeks Paid Time Off + 10 Paid Holidays

• Health, Dental, and Vision Insurance

• 401(k) with Matching

• Plus: Life Insurance, Mental Health Coverage, Health Advocate, and Gym Membership

We encourage you to apply even if your experience doesn't perfectly align with the job description as we seek out diverse and creative perspectives. Team members who love to learn and collaborate in an inclusive environment will thrive with us. We are an equal opportunity employer and do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status. If you need additional accommodations to feel comfortable during your interview process, please let us know at [email protected].