Senior Software Engineer, Bioinformatics
Senior software engineer leading the architecture of Variantyx's clinical whole-genome bioinformatics pipeline — a high-throughput production system written mainly in Python. Day to day: designing variant-detection algorithms, optimizing and refactoring pipeline code, and automating workflows under strict clinical quality standards.
- Compensation
- $120K–$170K / yr
- Location
- Massachusetts
- Work setup
- Not specified
- Seniority
- Senior
- Employment
- Not specified
- Experience
- 3+ years
- Category
- Software engineering
- Posted
Skills
Must have
- Master's in Computer Science, Mathematics, Computational Biology, or similar
- 3+ years of industry experience
- Production-grade software engineering experience and deep understanding of the SDLC
- Experience with pytest, mocking strategies, and writing modular, testable code
- Expert-level Python: internals, packaging, design patterns, writing clean Pythonic code
- Linux/Bash expertise: debugging complex Linux environments and writing robust shell scripts
- Production bioinformatics experience with FASTQ/BAM/CRAM/VCF file formats and variant calling algorithms and tools
- Experience with short- and long-read sequencing platforms
- Experience designing and implementing efficient MongoDB processes in a complex environment
Nice to have
- PhD in Computer Science, Mathematics, Computational Biology, or similar with 5+ years of industry experience
- TypeScript experience, to interface with the MongoDB data layer and execute workflows
- Rust experience, particularly for Python extensions (Maturin/PyO3); C++ experience acceptable if willing to learn Rust
- Database design experience with MongoDB and RDBMS: normalized schemas and data migrations
Full description
Compensation: $120k – $170k • 0.1% – 1.0%
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.
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