Senior Software Engineer, Data Pipelines

This role strongly prefers candidates located in the Boston area with the ability to regularly commute to our Seaport headquarters.

Due to the nature of this role, candidates should expect to support U.S. Government customers. Candidates must have the ability to obtain and maintain a U.S. security clearance per business requirements. In connection therewith, candidates must be willing to undergo a background investigation and meet eligibility requirements. Clearance sponsorship will be available.

Candidates who currently hold an active or recently inactive U.S. Government security clearance are encouraged to apply.

Ginkgo Biosecurity is building next-generation biosecurity infrastructure to help governments and partners detect, attribute, and deter biological threats. Our mission extends across public health, national security, and global defense, ensuring nations can rapidly identify dangerous pathogens, understand where threats originate, and respond with confidence.

On our Biosecurity team, you are a software engineer focused on building and operating critical biosecurity data systems. You design reliable data pipelines and models, productionize analytics, and ensure data quality across programs spanning PCR, sequencing, wastewater, biosurveillance, and large-scale environmental monitoring.

This role requires strong software engineering fundamentals—including system design, testing, and code quality—applied to data infrastructure challenges. You will work primarily on backend data systems, designing data warehouses, building ETL/ELT pipelines, and managing data architecture. The role combines platform engineering (e.g., orchestration with Airflow, observability, infrastructure-as-code) with analytics engineering (SQL modeling, testing, documentation) to deliver reliable data products that support threat detection, pathogen attribution, and operational decision-making.

Responsibilities

Data Platform Architecture & Engineering

• Plan, architect, test, and deploy data warehouses, data marts, and ETL/ELT pipelines primarily within AWS and Snowflake environments
• Build scalable data pipelines capable of handling structured, unstructured, and high-throughput biological data from diverse sources
• Develop data models using dbt with rigorous testing, documentation, and stakeholder-aligned semantics to ensure analytics-ready datasets

Data Quality & Governance

• Ensure data integrity, consistency, and accessibility across internal and external biosecurity data products
• Develop, document, and enforce coding and data modeling standards to improve code quality, maintainability, and system performance
• Serve as the in-house data expert, making recommendations on data architecture, pipeline improvements, and best practices; define and adapt data engineering processes to deliver reliable answers to critical biosecurity questions

API & Integration Development

• Build high-performance APIs and microservices in Python that enable seamless integration between the biosecurity data platform and user-facing applications
• Design backend services that support real-time and batch data access for biosecurity operations
• Create data products that empower public health officials, analysts, and partners with actionable biosecurity intelligence

AI & Data Democratization

• Democratize access to complex biosecurity datasets using AI and LLMs, making data more discoverable and usable for stakeholders
• Apply AI-assisted development tools to accelerate code generation, data modeling, and pipeline development while maintaining high quality standards

Cloud Infrastructure & Performance

• Build robust, production-ready data workflows using AWS, Kubernetes, Docker, Airflow, and infrastructure-as-code (Terraform/CloudFormation)
• Diagnose sy