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Bioinformatics Pipeline Test Engineer

Karwell Technologies

San Diego, CA

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JOB DETAILS
SKILLS
Amazon Simple Storage Service (S3), Amazon Web Services (AWS), Analysis Skills, Automation, Bioinformatics, Biology, Biotech and Pharmaceutical, Business Activity Monitoring (BAM), Cloud Computing, Communication Skills, Continuous Deployment/Delivery, Continuous Integration, Cross-Functional, Data Management, Data Quality, Data Sets, Debugging Skills, DevOps, Engineering, FDA (Food and Drug Administration), GCP (Good Clinical Practices), Genomics, Git, GitHub, Microsoft Windows Azure, Next Generation Sequencing (NGS), Problem Solving Skills, Python Programming/Scripting Language, Quality Assurance, Quality Engineering, Regression Testing, Requirements Management, Scripting (Scripting Languages), Statistics, System Test, Test Automation, Test Case, Test Design, Test Scripts, Test Strategy, Testing, Validation Testing
LOCATION
San Diego, CA
POSTED
2 days ago
Job Description:
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.
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.

Requirements:

  • 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 Skills:

  • Experience in 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.

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.

About the Company

K

Karwell Technologies

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