About Variantyx: Variantyx is an award-winning, technology-driven molecular diagnostics lab that offers innovative solutions in the genetic disorders, reproductive health, and precision oncology markets. Our proprietary whole genome analysis platform provides unparalleled diagnostic capabilities, enhances personalized treatment recommendations, shortens the time to diagnosis, and reduces healthcare costs.
About the Position: 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.
Responsibilities: • 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.
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 mongodb 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). Experience designing normalized schemas and performing data migrations.