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