Senior Software Engineer, Bioinformatics

Senior Software Engineer, Bioinformatics 1671 Worcester Road, Suite 400, Framingham, MA 01701, United States Salary: $130,000–$160,000 About the Company 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. About the Role We are looking for an experienced Senior Software Engineer to lead the architectural evolution of our core germline clinical bioinformatics pipeline. The production pipeline is a large‑scale, high‑throughput system written primarily in Python. This is a production engineering role; you will design and implement new variant detection modules, refactor legacy logic, and optimize performance while ensuring strict software quality standards in a highly‑regulated clinical environment. Responsibilities Lead performance engineering efforts, identify bottlenecks and optimization opportunities in the primary, secondary, and tertiary bioinformatics pipelines. Increase automation to scale sample throughput by automating business and production processes. Design, develop, validate, and deploy cutting‑edge algorithms for clinical‑grade variant detection using our CPU and GPU compute cluster. Translate business requirements into precise technical specifications and implement them, ensuring code supports business workflows and collaborates effectively with other teams. Maintain clean, well‑tested, well‑documented, and optimized production‑grade code. Required Qualifications Master’s in Computer Science, Mathematics, Computational Biology, or a related field. 3+ years of industry experience in production software engineering. Deep experience with the software development lifecycle (SDLC), pytest, mocking, and modular, test‑able code. Expertise in Python internals, packaging, design patterns, and writing clean, Pythonic code. Strong Linux/Bash skills – comfortable debugging complex interactions in a Linux environment and writing robust shell scripts. Production experience with standard bioinformatics file formats (FASTQ, BAM, CRAM, VCF) and variant calling algorithms; experience with short‑ and long‑read sequencing platforms. Strong architecture sense, including experience designing and implementing efficient MongoDB processes in a complex environment. Preferred Qualifications Ph.D. in Computer Science, Mathematics, Computational Biology, or a related field with 5+ years of industry experience. Experience writing TypeScript to interface with MongoDB and execute workflows. Experience writing Rust, especially for Python extensions (Maturin/PyO3); C++ experience acceptable if willing to learn Rust. Database design experience with MongoDB and relational database management systems (RDBMS), including schema design and migrations. Benefits Employee Stock Options Plan (ESOP) Paid Time Off (PTO) Medical, Dental, Vision, Life, and Disability insurance 401(k) Retirement Savings Plan Location and Work Arrangement This is a remote or hybrid position. Candidates must live in the United States. Application Statement Join our rapidly growing organization and help build the software that powers the future of whole‑genome diagnostics. #J-18808-Ljbffr 360Dx