Software Engineer – Bioinformatics Pipelines

This is a fully remote position, open to applicants in Illinois.

📋 Description

• Ensure the software quality of genomics pipelines operating within the customer's on-premise HPC environment is maintained and enhanced.

• Optimize pipeline performance in the HPC setting.

• Automate operational processes and recurring engineering tasks for pipelines.

• Offer operational support, troubleshoot issues, and resolve challenges related to the transfer and delivery of genomic data.

• Execute and uphold integrations between pipelines, laboratory systems, and sequencing instruments.

• Establish and maintain the technical infrastructure that facilitates the movement, analysis, and delivery of genomic data in collaboration with the customer's bioinformatics team.

• Assist with the increased pipeline workload resulting from the transition of the LIS from Soft to Epic Beaker.

• Engage as a fully integrated member of an agile pipeline team throughout the project duration.

• Collaborate closely with the delivery team and customer stakeholders from initial project definition to final delivery.

⛳️ Requirements

• Professional experience in software engineering with a proven track record in bioinformatics pipeline engineering.

• Practical experience in production environments using Python, Bash, and Nextflow.

• Strong foundational knowledge in software engineering applied to bioinformatics pipelines, emphasizing software quality, performance tuning, automation, and operational support.

• Proficiency in both Python and Bash programming languages.

• Experience with Nextflow for managing workflows.

• Experience in developing, tuning, and managing pipelines within an on-premise high-performance computing (HPC) environment.

• Familiarity with integrating software with laboratory systems and sequencing instruments.

• Experience as part of an agile team.

• Ability to quickly integrate into an established team and contribute effectively with minimal ramp-up time.

• Direct experience with sequencing platforms such as Illumina, Oxford Nanopore, or PacBio is considered a valuable qualification.

🏝️ Benefits

• Comprehensive benefits package.

• Opportunities for professional development and growth.

• Collaborative and innovative work environment.