Key skills
Pythonpytestmocking strategiesmodular testable codeLinuxBashshell scriptingbioinformaticsFASTQBAMCRAMVCFvariant calling algorithmsshort-read sequencinglong-read sequencingsoftware development lifecyclesoftware architectureTypescriptMongoDBRustC++relational database management systemsdatabase designdata migrationsTypeScriptCShellPytestSDLC
About this role
Variantyx is a rapidly growing, engineering-driven organization focused on whole genome diagnostics. They are seeking a Senior Software Engineer to lead the architectural evolution of their core germline clinical bioinformatics pipeline, focusing on performance engineering, automation, and feature development.
Responsibilities:
- Identify bottlenecks and opportunities for optimization in our core primary, secondary, and tertiary bioinformatics pipelines
- You will help scale sample throughput by automating business processes, from tasks in the development lifecycle to tasks in the production workflow
- 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
Requirements:
- 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
- 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