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

Learn more about this Employer on their Career Site

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