Bioinformatics Pipeline Test Engineer Healthcare San Diego CA Local to CA or who can relocate

Vytwo; Prosper (TX); On-site; USD 110,000 - 150,000; Full time

Job summary

Vytwo in San Diego, CA is seeking a Bioinformatics Test Engineer to validate NGS data pipelines and workflows. You will bridge bioinformatics expertise with QA and automation to ensure data quality and reliability.

The role emphasizes testing strategies for alignment, variant calling, and annotation, with Python scripting and CI/CD workflows. Collaboration across teams and exposure to cloud environments are expected.

Qualifications

• Must have bioinformatics experience in testing or QA.
• Strong Python scripting and data validation skills.
• Hands-on with Git, CI/CD and cloud workflows.

Responsibilities

• Design and execute testing strategies for NGS pipelines (alignment, variant calling).
• 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.

Skills

Bioinformatics

Genomics

NGS workflows

Python scripting

Testing mindset

Data validation

Communication

Problem solving

Tools

Git

CI/CD pipelines

Nextflow

Snakemake

Cloud platforms

Job description

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