Bioinformatics Software Engineer

7 months ago

Boston, MA, USASenior

Responsibilities

Design, implement, and maintain bioinformatics pipelines for alignment, quality control, and variant calling from high-throughput WGS and RNA-Seq data.
Build reproducible, tested, and automated workflows using CWL and containerize them with Docker.
Architect and manage AWS compute infrastructure, including automated deployment, scaling, and monitoring.
Integrate version control, automated testing, and deployment workflows to support data integrity and reliable pipeline execution.
Develop utility tools for metadata management, file integrity checks, file conversion, and integration with the SMaHT Data Portal.
Collaborate with research scientists, engineers, and IT teams to refine requirements and deliver software solutions.
Document code, workflows, and infrastructure configurations.

At least five years of post-secondary education or relevant work experience.
PhD in computational biology, bioinformatics, statistics, computer science, or another quantitative field is strongly preferred.
Strong programming skills, especially in Python and shell scripting.
Extensive experience analyzing high-throughput sequencing data and using tools for sequence alignment, variant calling, and sequence-data quality control.
Proficiency with Docker and the Workflow Description Language/CWL for reproducible workflow execution and orchestration.
Strong understanding of AWS services such as EC2 and S3, or similar cloud platforms.
Experience with Git, automated testing, deployment workflows, Linux systems, HPC, and distributed computing environments.
Knowledge of optimizing pipelines for large-scale genomic projects.

One-year term appointment from the date of hire, with possible extension based on performance and continued funding.
35-hour standard work week.
Remote and hybrid work arrangements may be available, with schedule and location determined by the department; hybrid work must be performed in a Harvard-registered state when outside Harvard locations.
Comprehensive benefits include paid time off, parental leave, medical, dental, and vision insurance beginning on day one, retirement contributions, wellbeing resources, family and caregiver support, professional development and tuition assistance, commuter benefits, discounts, and campus perks.