Bioinformatics Software Engineer II

Ambry Genetics • Aliso Viejo, CA

310d • $111,000 - $145,000 • Remote

About The Position

The Bioinformatics Engineer II is responsible for developing and maintaining computational pipelines for processing clinical sequencing data from customers. This position focuses on implementing robust, scalable bioinformatics solutions using Nextflow, Python, and AWS technologies. This role requires technical proficiency to ensure reliable processing and analysis of customer sequencing data while adhering to quality standards and performance benchmarks.

Requirements

• Bachelor's degree in bioinformatics, computer science, or related discipline
• At least 3+ years of relevant industry experience
• Strong proficiency with Python programming and Linux environments
• Experience with Nextflow or similar workflow management systems
• Experience with Illumina sequencing data and bioinformatics NGS pipelines
• Knowledge of version control systems, particularly Git
• Demonstrated ability to solve problems independently
• Experience with bioinformatic data formats and processing methods
• Familiarity with AWS cloud services
• Ability to work effectively in a collaborative environment
• Experience with software testing methodologies
• Strong analytical and debugging skills

Nice To Haves

• Advanced degree in bioinformatics, computer science, or related disciplines
• Experience with clinical genomics
• Experience with Docker and containerized applications
• CI/CD pipeline experience
• Experience working in a cloud environment (AWS)
• Experience working in a regulated setting

Responsibilities

• Develop and maintain bioinformatics data pipelines using Nextflow and Python
• Implement cloud-based solutions utilizing AWS services for efficient data processing
• Refactor existing pipelines to improve performance, maintainability, and scalability
• Apply software development best practices including version control, testing, and documentation
• Troubleshoot and resolve complex technical issues independently
• Design and develop new pipeline components and data analysis methods
• Collaborate with cross-functional teams to implement clinical requirements
• Maintain code quality through code reviews and adherence to coding standards
• Monitor pipeline performance and implement optimizations
• Other duties as assigned

Benefits

• $111,000 - $145,000 per year
• Eligible for a Short-Term Incentive Plan with the target at 7.5% of annual earnings

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Industry: Ambulatory Health Care Services
• Education Level: Bachelor's degree