Bioinformatics Software Engineer

Company Description

By working at Harvard University, you join a vibrant community that advances Harvard's world-changing mission in meaningful ways, inspires innovation and collaboration, and builds skills and expertise. We are dedicated to creating a diverse and welcoming environment where everyone can thrive.

Harvard Medical School's mission is to nurture a diverse, inclusive community dedicated to alleviating suffering and improving health and well-being for all through excellence in teaching and learning, discovery and scholarship, and service and leadership. You’ll be at the heart of biomedical discovery, education, and innovation, working alongside world‑renowned faculty and a community dedicated to improving human health. This is more than a job – it’s an opportunity to shape the future of medicine.

Participate in the design of software that supports and enriches research productivity and reliability; implement software solutions. Develop software and data services with researchers to ensure that modern standards of reproducible code are kept.

• Design, implement, and maintain bioinformatics pipelines for high‑throughput sequencing data (e.g., alignment, QC, variant calling from WGS and RNA‑seq) similar to those in existing repositories: ‑pipes.
• Build reproducible, well‑tested, and automated workflows using workflow management systems (particularly CWL).
• Architect and manage AWS‑based compute infrastructure to support pipeline execution, including automated deployment, scaling, and monitoring.
• Containerize workflows using Docker or similar tools for managed execution and portability.
• Integrate CI/CD tooling to automate testing, deployment, and version control to ensure data integrity and correct execution of the pipeline.
• Develop utility tools for metadata management, file integrity checks or conversion (e.g., VCF, BAM to CRAM), and integration with the SMaHT Data Portal.
• Collaborate cross‑functionally with research scientists, engineers, and IT teams to refine requirements and deliver high‑quality solutions.
• Document code, workflows, and infrastructure configurations clearly.

• Minimum of five years’ post‑secondary education or relevant work experience.

• PhD in computational biology/bioinformatics/statistics/CS or another quantitative field is strongly preferred.
• Superb programming skills, especially in Python and shell scripting, and communication skills are strongly preferred.
• Extensive experience with analysis of high‑throughput sequencing data and knowledge of bioinformatics tools for sequence alignment, variant calling, sequence data QC, etc.
• Proficiency in Docker for creating a reproducible execution environment and Workflow Description Language for orchestrating complex tasks.
• Strong understanding of AWS services (EC2, S3) or similar cloud platforms for compute and storage.
• Version control & CI/CD:
  Git, automated testing, deployment workflows.
• Experience with Linux systems, HPC, and distributed computing environments.
• Knowledge of optimizing pipelines for large‑scale genomic projects.

• Appointment End Date:
  This is a one‑year term position from the date of hire, with the possibility of extension, contingent upon work performance and continued funding to support the position.
• Standard Hours/
  
  Schedule:
  
  35 hours per week.
• Visa Sponsorship Information:
  Harvard University is unable to provide visa sponsorship for this position.
• Pre‑Employment Screening:
  Identity.
• Other Information:
  Please note that we are currently conducting a majority of interviews and onboarding remotely and virtually. We appreciate your understanding.
• Staying Informed About Your Application:
  Due to the high volume of applications, we may not always be able to reach out right away, but you can track your status anytime through the Careers@Harvard portal.

This position has been determined by school or unit leaders that some of the duties and responsibilities can be effectively performed at a non‑Harvard location. The work schedule and location…