Bioinformatics Pipeline Test Engineer (Healthcare)

Location: San Diego, CA
Experience: 2+ Years
Employment Type: Contract

Position Overview:

We are looking for a Bioinformatics Pipeline Test Engineer to validate and ensure the quality, accuracy, and reliability of NGS data pipelines and bioinformatics workflows.

The ideal candidate will have a strong combination of bioinformatics/genomics knowledge, software testing, Python automation, and data pipeline experience . This role will involve testing NGS workflows, validating genomic data, identifying defects and discrepancies, and collaborating with engineering and cross-functional teams to ensure production-quality solutions.

Key Responsibilities:

• Design and execute testing strategies for NGS pipelines , including alignment, variant calling, and annotation workflows.
• Perform data validation, regression testing, and discrepancy analysis across bioinformatics pipelines.
• Develop automated test scripts and validation utilities using Python .
• Translate functional and technical requirements into comprehensive test cases and validation criteria.
• Validate genomic data formats and processing workflows, including FASTQ, BAM, and VCF .
• Identify, document, troubleshoot, and track pipeline defects and data quality issues.
• Work with CI/CD pipelines and cloud-based data workflows to support automated testing and deployment.
• Collaborate with bioinformatics engineers, data engineers, developers, and QA teams to improve pipeline quality and reliability.
• Support testing of production and cloud-based data pipelines and help troubleshoot issues across environments.

Must-Have Skills:

• 2+ years of relevant experience in bioinformatics, genomics, data pipeline testing, or QA.
• Strong understanding of Next Generation Sequencing (NGS) workflows.
• Hands-on experience with FASTQ, BAM, and/or VCF data formats.
• Experience in bioinformatics pipeline testing, QA, validation, or data testing .
• Strong Python scripting/automation skills.
• Hands-on experience with Git and CI/CD tools.
• Experience working with cloud platforms such as AWS, GCP, or Azure .
• Understanding of data pipelines and automated testing frameworks.
• Strong analytical, troubleshooting, and problem-solving skills.
• Excellent communication and collaboration skills.

Preferred Qualifications:

• Experience in the biotechnology, healthcare, genomics, or life sciences industry.
• Familiarity with workflow orchestration tools such as Nextflow, Snakemake, WDL, or Cromwell .
• Experience with variant calling and genomic data validation.
• Exposure to regulated environments such as FDA or CLIA .
• Experience working with cloud-based bioinformatics pipelines.
• Knowledge of reference/golden datasets for data validation.
• Experience with automated regression testing and pipeline validation.