Bioinformatics Operations Support Engineer (Hybrid)

Job Description

As a Bioinformatics Engineer, you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing.

This position is in our Bioinformatics Operations group, part of the Research and Development organization, in Advanced Diagnostics based in San Juan Capistrano, CA. This position is intended to be either on site or hybrid – working on site at least 2-3 days per week in our San Juan Capistrano, CA lab.  The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment, using short and long-read sequencing as the basis of evidence.  The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate.  The Bioinformatics Operations group supports, hones, and executes the processes defined by our Engineering and Lab Operations groups with emphasis on compliance and continuous improvement.  While coupled tightly to regulation through standards in validation, documentation, and data retention, the group is an integral part of the development cycle of our analysis workflows and visualization.

This professional will work in a hybrid capacity with 3 days onsite at our San Juan Capistrano, CA facility. Additionally, our Marlborough, MA location is an option as well.

• Support production day-to-day operations, quickly pivoting focus to respond to incidents and requests
• Monitor, execute, and improve sequence analysis workflows and automation
• Track, troubleshoot and mitigate issues encountered in processing production samples to meet strict Turnaround Times (TAT) and business SLAs
• Plan and develop solutions to recurring issues to be merged back into development branch maintained by the Engineering group
• Generate, wrangle, merge and glean information from varied and complex data sets
• Use of RESTful APIs linked to various systems including LIMS, AWS job runners and other systems necessary for data processing and execution
• Design and perform validation, testing, and production deployment of systems and software to standardize processes across all Quest Diagnostics genetic testing labs
• Design and perform analytical validation analysis for new genomic testing products
• Write and maintain production documentation for compliance and supportability of all bioinformatics processes in production environment
• Produce charts and visualization for dashboards, reporting, and in support of data driven hypothesis testing
• Support interface, integration, and testing projects
• Utilize a Software Development Life Cycle documentation procedure
• Be an active team player and support the group
• Accept input on solutions from other colleagues and teams
• Availability for on-call support

The ideal candidate will have a history of using bioinformatic technical skills to deliver accurate and timely results.

Required:

• 5 yr experience using formal programming and scripting languages
• 5 yr experience working on a Linux command-line to process, parse, and merge varied data sets
• 3 yr experience working with web services and utilizing API communications (REST, SOAP, etc)
• 3 yr experience in a distributed cloud HPC environment 
• Knowledge and understanding of genomics, next-generation sequencing, and bioinformatics including parsing and working with typical file formats (FASTQ, BAM, VCF)
• Experience supporting production grade software
• Experience with source control in a development, testing, and production environment
• Experience communicating technical results and data
• Experience working with APIs to pull/query data

Preferred:

• Automated testing experience; CI/CD experience preferred
• Knowledge of CAP documentation requirements or working in a regulated environment a plus
• Microsoft UI: Access, VBA, Macros
• Pipeline Workflow Manager: Nextflow
• CI/CD in GitHub

Education:

• Required: B.S. in Computer Science, Software Engineering, Bioinformatics, or a related field.
• Preferred: MSc/PhD degree in Computer Science, Software Engineering, Bioinformatics

Preferred Technical Training:

• Agile certification
• Nextflow training
• Cloud Computing
• Data Science