Senior Software Engineer, Bioinformatics

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 fully vertically integrated pipeline 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.

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About the Role

We are looking for an experienced 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 written primarily in Python . We continue to push the frontier of diagnostic capabilities while also heavily scaling our operations. As part of a small team, you will be expected to take ownership of your work, and to provide clean, well-tested, well-documented, optimized code.

This is not a research position; it is a production engineering role. You will not just be running tools; you will be designing and implementing new variant detection modules, supporting and refactoring legacy logic, and identifying key areas for optimization. In addition to translating business requirements into precise technical specifications and implementing them, you will be expected to understand how your code supports our business workflows and how your code affects other teams. Working in a highly-regulated clinical environment means enforcing strict software quality standards to ensure our clinical results are accurate and reproducible, every single time.

What You Will Do

• Performance Engineering: Identify bottlenecks and opportunities for optimization in our core primary, secondary, and tertiary bioinformatics pipelines.
• Increase Automation: You will help scale sample throughput by automating business processes, from tasks in the development lifecycle to tasks in the production workflow.
• Feature Development: You will design, develop, validate, and deploy cutting-edge algorithms for clinical-grade variant detection, making use of our high-performance CPU and GPU compute cluster.

Required Qualifications

Master's in Computer Science, Mathematics, Computational Biology, or similar. 3+ years of industry experience.

• Production Software Engineering: You are experienced developing production-grade software. You understand the Software Development Lifecycle (SDLC) deeply. You are experienced with pytest, mocking strategies, and writing modular, testable code.
• Python Mastery: You are an expert in Python internals, packaging, and design patterns. You know how to untangle complex dependencies and write clean, Pythonic code.
• Linux/Bash Expert: You live in the terminal. You are comfortable debugging complex interactions in a Linux environment and writing robust shell scripts.
• Bioinformatics Expertise: Production experience, and significant experience with standard file formats (FASTQ / BAM / CRAM / VCF) and variant calling algorithms and common tools. Experience with short- and long-read sequencing platforms. 
• Strong Architecture Sense: You have experience designing and implementing efficient new processes in a complex environment.

Preferred Qualifications

PhD in Computer Science, Mathematics, Computational Biology, or similar. 5+ years of industry experience.

• Typescript Experience: Experience writing Typescript, to interface with our MongoDB data layer and execute workflows.
• Rust Experience: Experience writing Rust, particularly for Python extensions (Maturin/PyO3). C++ experience is also acceptable if you are willing to learn Rust. 
• Database Design: Experience with MongoDB and Relational Database Management Systems (RDBMS). xhyhwjd Experience designing normalized schemas and performing data migrations.

Compensation and Benefits

• Employee Stock Options Plan (ESOP)
• Paid Time Off (PTO)
• Medical, Dental, Vision, Life, and Disability insurance
• 401k Retirement Savings Plan