Bioinformatics Associate I

ApTask Global Workforce (AGW) is seeking a Bioinformatics Associate I with a technology company. This is a 8+ month contract opportunity with our client located in South San Francisco, CA. This is a hybrid position.

Summary:

This role supports software systems and data workflows within a Next-Generation Sequencing (NGS) laboratory environment. The successful candidate will develop, maintain, and support applications and pipelines used for sequencing data processing, laboratory workflow management, and data analysis. This role requires a strong background in software development, database management, and workflow automation, collaborating closely with bioinformaticians, scientists, and laboratory staff to ensure reliable data processing and scalable analysis pipelines.

Responsibilities:

• Design, develop, test, and maintain Java and Java EE web applications to support sequencing lab workflows
• Develop software tools to support sequencing data processing, data tracking, and laboratory operations
• Develop and maintain bioinformatics pipelines for processing NGS data using WDL (Workflow Description Language)
• Manage and support workflow execution through the Cromwell workflow engine
• Develop and execute SQL and PL/SQL queries to support data retrieval, transformation, and system integration
• Support Oracle database systems, including writing queries, performing updates, and maintaining database integrity
• Develop and maintain Python and Bash scripts to automate data processing and analysis workflows
• Integrate laboratory information systems (LIMS) with sequencing platforms and analysis pipelines
• Support deployment and execution of pipelines in High Performance Computing (HPC) environments
• Monitor and troubleshoot pipeline execution issues and system performance problems
• Provide technical support to scientists and lab personnel

Requirements:

• Bachelor's or master's degree in computer science, Bioinformatics, Computational Biology, Software Engineering, or related field
• Minimum of 3 years of relevant experience
• Strong experience with Oracle databases
• Proficiency in SQL and PL/SQL
• Experience with Java and Java EE web application development
• Strong programming skills in Python
• Experience with Bash scripting
• Experience developing or supporting workflow pipelines using WDL
• Familiarity with the Cromwell execution framework
• Experience working with data processing pipelines or scientific data systems

Desired skills:

• Experience working in NGS sequencing or genomics environments
• Familiarity with bioinformatics data processing workflows
• Experience working in HPC computing environments
• Experience with AWS cloud services
• Experience with container technologies (Docker, Singularity, etc)
• Experience using Git version control systems
• Experience supporting LIMS systems or laboratory data platforms
• Strong problem-solving and troubleshooting skills
• Ability to work independently in a fast-paced research environment
• Strong communication skills and ability to collaborate with scientific teams

Pay range: Up to $58.68 per Hour

Only candidates available and ready to work directly as ApTask Global Workforce (AGW) employees will be considered for this position.

If you have the described qualifications and are interested in this exciting opportunity, please apply!

ApTask Global Workforce (AGW)

ApTask Global Workforce (AGW) is a certified Minority and Veteran workforce solutions company. AGW delivers operational, clinical, lab and professional talent with a strong focus on healthcare and life sciences. The company supports clients with reliable staffing, program expertise and a commitment to quality, speed and consistent delivery.

Benefits of working with ApTask Global Workforce include:

• Medical
• Dental
• Vision
• Sick Pay (for applicable states/municipalities)

Our team stays close to the process and is here to guide you every step of the way. To learn more, please visit our website

ApTask Global Workforce is an Equal Opportunity Employer. Candidates will receive consideration without regard to their race, color, religion, sex, sexual orientation, gender identity, national origin, disability or status as a protected veteran.