Software Guidance & Assistance, Inc., (SGA), is searching for a
Bioinformatics Software Engineer - NGS Sequencing Systems for a
contract assignment with one of our premier Pharmaceutical services clients in
South San Francisco, CA.
Responsibilities :
We are seeking a highly motivated Bioinformatics Software Engineer to support 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, with experience supporting scientific data systems. The candidate will collaborate closely with bioinformaticians, scientists, and laboratory staff to ensure reliable data processing and scalable analysis pipelines.
- Software Development
- Design, develop, test, and maintain Java and Java EE web applications used to support sequencing lab workflows and laboratory data systems.
- Develop software tools to support sequencing data processing, data tracking, and laboratory operations.
- Participate in software design discussions and contribute to scalable and maintainable system architecture.
- Workflow & Pipeline Development
- Develop and maintain bioinformatics pipelines for processing NGS data.
- Implement workflow automation using WDL (Workflow Description Language).
- Manage and support workflow execution through the Cromwell workflow engine.
- Optimize pipeline performance and ensure efficient processing of large sequencing datasets.
- Database & Data Management
- 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.
- Ensure reliable data storage, accessibility, and traceability across sequencing workflows.
- Data Processing & Automation
- Develop and maintain Python and Bash scripts to automate data processing, analysis workflows, and system integration tasks.
- Implement data validation and quality checks to ensure accuracy and consistency of sequencing data.
- Systems Integration
- Integrate laboratory information systems such as LIMS with sequencing platforms and downstream analysis pipelines.
- Support data flow between laboratory instruments, analysis systems, and databases.
- Infrastructure & Deployment
- Support deployment and execution of pipelines in High Performance Computing (HPC) environments.
- Assist with cloud-based workflow deployment using AWS services.
- Build and maintain containerized software environments (e.g., Docker) to ensure reproducibility of computational workflows.
- Troubleshooting & Support
- Monitor and troubleshoot pipeline execution issues and system performance problems.
- Identify and resolve bottlenecks in data processing pipelines.
- Provide technical support to scientists and lab personnel using the software systems.
- Collaboration
- Work closely with bioinformaticians, data scientists, software engineers, and laboratory staff to understand workflow requirements.
- Translate scientific and operational needs into scalable software solutions.
- Participate in cross-functional discussions to improve sequencing workflow efficiency.
- Documentation & Best Practices
- Maintain clear documentation of pipelines, applications, and database structures.
- Use Git repositories and version control best practices to manage software development.
- Support testing, validation, and continuous improvement of systems.
Required Skills:
- Bachelor's or Master's degree in Computer Science, Bioinformatics, Computational Biology, Software Engineering, or related field w/ MIN 3 years exp
- 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.
- 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.
- Ability to manage multiple priorities and support complex data workflows.
Preferred Skills:
- Experience with NGS sequencing workflows and bioinformatics tools is highly desirable, but not required.
- 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.
SGA is a technology and resource solutions provider driven to stand out. We are a women-owned business. Our mission: to solve big IT problems with a more personal, boutique approach. Each year, we match consultants like you to more than 1,000 engagements. When we say let's work better together, we mean it. You'll join a diverse team built on these core values: customer service, employee development, and quality and integrity in everything we do. Be yourself, love what you do and find your passion at work. Please find us at .
SGA is an Equal Opportunity Employer and does not discriminate on the basis of Race, Color, Sex, Sexual Orientation, Gender Identity, Religion, National Origin, Disability, Veteran Status, Age, Marital Status, Pregnancy, Genetic Information, or Other Legally Protected Status. We are committed to providing access, equal opportunity, and reasonable accommodation for individuals with disabilities in employment, and our services, programs, and activities. Please visit our company to request an accommodation or assistance regarding our policy.
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