Senior Software Engineer, Bioinformatics (Rust and Python)

About Variantyx

Join our rapidly growing, engineering-driven organization and help build the software that powers the future of whole-genome diagnostics. Backed by leading life sciences investors, we have achieved industry-leading diagnostic yield and unit economics through a vertically integrated software stack that spans from sample to report. At the core of our success is a proprietary clinical platform that uniquely enables our workflows, allowing us to solve complex biological data challenges at scale. With a strong global presence across our internal teams and external partnerships, we offer the stability of a well-funded industry leader combined with the agility of a high-growth tech company.

Be one of the first applicants, read the complete overview of the role below, then send your application for consideration.

About the Role

We are looking for an experienced, production-focused Senior Software Engineer to lead the architectural evolution of our core germline clinical bioinformatics pipeline.

Our production pipeline is a large-scale, high-throughput system. We continue to push the frontier of diagnostic capabilities while heavily scaling our operations. As part of a lean, high-caliber engineering team, you will take ownership of complex technical challenges, delivering clean, rigorously tested, and heavily optimized code.

Important Note: This is strictly a production software engineering role, not an academic research, data science, or scripting position. We are specifically looking for highly technical engineers with a strong Computer Science background who build robust, high-performance systems. If your primary experience is writing R or Python scripts for data analysis or academic research, this role will not be a fit.

What You Will Do

• High-Performance Engineering: Identify bottlenecks and rewrite/optimize core primary, secondary, and tertiary bioinformatics pipelines utilizing Rust for maximum performance and memory safety.
• Systems Integration: Seamlessly bridge high-performance Rust modules with our existing Python infrastructure using tools like PyO3 and Maturin.
• Database Architecture: Design, implement, and scale complex database schemas (MongoDB and RDBMS) to manage massive, high-throughput genomic datasets efficiently.
• Clinical-Grade Feature Development: Design, develop, validate, and deploy cutting-edge algorithms for variant detection and scoring on our high-performance CPU and GPU compute clusters.
• Production Quality Assurance: Enforce strict software quality standards, SDLC best practices, and automated testing to ensure our clinical results are perfectly accurate and reproducible in a highly regulated environment.

Required Qualifications

• Education & Experience: Master’s or Bachelor’s degree in Computer Science, Software Engineering, or a closely related technical field, backed by 5+ years of dedicated industry experience in production software engineering.
• Rust & Python Expertise: You are an expert in both Rust and Python. You understand Python internals, packaging, and design patterns, and you are highly proficient in writing memory-safe, concurrent Rust code (including Python extensions).
• Database Architecture: Strong background in database design, data modeling, and performance tuning. You have deep experience with MongoDB, relational databases (RDBMS), normalized schemas, and complex data migrations.
• Production Engineering Rigor: You do not write "scripts"; you build systems. You have deep expertise in the Software Development Lifecycle (SDLC), testing frameworks, mocking strategies, and writing modular, deployable code.
• Bioinformatics Domain Knowledge: Strong production experience working with standard genomic file formats (FASTQ / BAM / CRAM / VCF), variant calling algorithms, and high-throughput sequencing platforms (short- and long-read).
• Linux/Bash Mastery: You are highly comfortable debugging complex systems interactions in a Linux environment and writing robust shell automation.

Preferred Qualifications

• Advanced Degree: PhD in Computer Science, Software Engineering, or closely related field.
• Typescript: Experience writing Typescript to interface with our MongoDB data layer and execute workflows.

Compensation and Benefits

• Salary minimum $120,000 - based on experience
• Employee Stock Options Plan (ESOP)
• Paid Time Off (PTO)
• Medical, Dental, Vision, Life, and Disability insurance
• 401k Retirement Savings Plan