Software Engineer – Bioinformatics Pipelines

OnTrac Solutions is seeking a Software Engineer with bioinformatics pipeline expertise for a 12- to 18-month contractor engagement supporting a healthcare genomics customer. The role focuses on maintaining, improving, tuning, automating, and operationally supporting genomic pipelines, as well as integrating them with laboratory systems and sequencing instruments during an LIS transition from Soft to Epic Beaker.

Responsibilities:

• Maintain and improve the software quality of the genomics pipelines running in the customer's on-premise HPC environment
• Tune the performance of the pipelines in the HPC environment
• Automate pipeline operations and recurring engineering tasks
• Provide operational support for the pipelines, including troubleshooting failures and resolving issues in the movement and delivery of genomic data
• Implement and maintain integrations between the pipelines and laboratory systems and sequencing instruments, including Illumina, Oxford Nanopore, and PacBio platforms
• Implement and maintain the technical infrastructure that enables the movement, analysis, and delivery of genomic data, working alongside the customer's bioinformatics team, which owns the biological aspects of the analyses
• Support the additional pipeline workload arising from the organization-wide LIS transition from Soft to Epic Beaker
• Participate as a full member of an agile pipeline team for the duration of the engagement

Requirements:

• Professional software engineering experience with a demonstrated background in bioinformatics pipeline engineering
• Hands-on production experience with Python, Bash, and Nextflow
• Strong software engineering fundamentals applied to bioinformatics pipelines, with a focus on software quality, performance tuning, automation, and operational support
• Proficiency in Python and Bash
• Experience with Nextflow for workflow management
• Experience developing, tuning, and operating pipelines in an on-premise high-performance computing (HPC) environment
• Experience integrating software with laboratory systems and sequencing instruments
• Experience working as a member of an agile team
• Ability to integrate into an established team quickly and contribute with limited ramp-up
• Direct experience with Illumina, Oxford Nanopore, or PacBio sequencing platforms