Bioinformatics Software Engineer – NGS Sequencing Systems

Job title: Bioinformatics Software Engineer NGS Sequencing Systems
Duration: till end of year

Location: South SFO CA

Position Summary
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.
Experience with NGS sequencing workflows and bioinformatics tools is highly desirable but not required.

Key Responsibilities
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 Qualifications
Bachelors or Masters 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.

Preferred Qualifications
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.

Skills & Competencies
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.

Interview process: 1. phone (15-20mins) 2. In-person (1 hr)
Hybrid- 2-3 days onsite
Function: gRED