Bioinformatics Pipeline Engineer

Who is Recruiting from Scratch :

Recruiting from Scratch is a talent firm that focuses on placing the best candidate for our clients. Our team is 100% remote and we work with teams across North America, South America, and Europe to help them hire.

Bioinformatics Pipeline Engineer

Location: South San Francisco, CA
Company Stage: Series A Biotech Company
Office Type: Onsite
Salary Range: $155,000 - $200,000 + Equity

Company Description
Our client is a rapidly growing, venture-backed biotech company revolutionizing DNA sequencing services. Their innovative technology enables overnight sequencing of whole plasmids, bacterial genomes, and colonies without primers or minipreps. With a global network of labs and thousands of daily users including leading scientists and biotech innovators, they're accelerating scientific discoveries that contribute to a healthier planet.

What You Will Do

• Design and develop robust bioinformatics pipelines focusing on Oxford Nanopore sequencing data
• Drive optimization of pipeline performance, reliability, and scalability using industry best practices
• Collaborate with cross-functional teams of scientists and engineers to implement specific pipeline goals
• Troubleshoot complex biological and sequencing artifacts while maintaining high coding standards
• Provide technical leadership in pipeline usage and support training initiatives
• Evaluate and integrate cutting-edge bioinformatics tools to enhance pipeline capabilities

Ideal Candidate Background

• 3+ years of experience developing production-grade bioinformatics pipelines
• Advanced degree in Bioinformatics, Biostatistics, or related field
• Strong foundation in workflow languages, particularly Snakemake or Nextflow
• Hands-on experience with Oxford Nanopore and Illumina sequencing technologies
• Demonstrated expertise in Python, Bash, Conda, AWS, and GitHub Actions
• Track record of building and optimizing pipelines for commercial applications

Preferred Qualifications

• Experience with Docker/Apptainer/Singularity containerization
• AWS cloud infrastructure knowledge (Lambda, S3, RDS)
• Background in developing REST APIs
• Experience in a fast-paced biotech environment

Compensation & Benefits

• Competitive salary range: $155,000 - $200,000
• Equity through Employee Stock Options
• Comprehensive health, dental, and vision coverage
• 401(k) with company matching
• 4 weeks PTO + 10 paid holidays
• Mental health benefits and gym membership
• Professional development opportunities

Join a dynamic team that's pushing the boundaries of DNA sequencing technology. This role offers the opportunity to make a significant impact in a rapidly growing field while working with cutting-edge technologies.