Title: Bioinformatics Pipeline Test Engineer
Domain: Healthcare
Location: San Diego, CA - Local to CA or who can relocate
Duration: 6 Months
Experience: 2+ years
Must have:
- Bioinformatics OR Genomics
- NGS OR "Next Generation Sequencing"
- VCF OR BAM OR FASTQ
- Python
- Testing OR QA OR "Quality Engineer" OR Validation
- Git
Job Description:
Role Overview
We are seeking a Bioinformatics Test Engineer to validate and ensure the quality of NGS data pipelines and bioinformatics workflows. The role requires a strong blend of bioinformatics knowledge, QA expertise, and automation skills.
Key Responsibilities
• Design and execute testing strategies for NGS pipelines (alignment, variant calling, annotation)
• Perform data validation, regression testing, and discrepancy analysis
• Develop automated test scripts (Python)
• Translate requirements into test cases and validation criteria
• Work with CI/CD pipelines and cloud-based workflows
• Collaborate with cross-functional teams to ensure data accuracy and reliability
Required Skills
• Strong understanding of NGS workflows (FASTQ, BAM, VCF)
• Experience in bioinformatics pipeline testing or QA
• Proficiency in Python scripting
• Hands-on with Git and CI/CD tools
• Experience with cloud platforms (AWS/GCP/Azure) and data pipelines
• Strong problem-solving and communication skills
Preferred
• Experience in the biotech/life sciences domain
• Familiarity with Nextflow, Snakemake, or similar workflows
• Exposure to regulated environments (CLIA/FDA)
What We’re Looking For
• Strong testing mindset + hands-on engineering skills
• Ability to debug pipelines and explain thought process clearly
• Experience with real-world data workflows (not just academic projects)
• Mentions NGS pipelines + testing together
• Has Python + Git + CI/CD
• Mentions variant calling / VCF validation
• Worked on cloud or production pipelines
Reject or deprioritize if:
• Only academic bioinformatics (no testing/QA)
• Only statistics validation (no system testing)
• No Python or automation
• No infra experience (cloud / CI/CD / DB)
• Only local scripts, no real pipelines
Other High Priority Keywords
- Variant Calling
- Pipeline Testing
- Regression Testing
- Test Strategy OR Test Case Design
- Data Validation
- Golden Dataset OR Reference Dataset
- CI/CD OR "GitHub Actions" OR GitLab OR "Azure DevOps"
- AWS OR S3 OR Cloud
- Nextflow OR Snakemake OR WDL OR Cromwell
- Automation Testing