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:
• 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 will be set…