Bioinformatics Pipeline Test Engineer (Healthcare)

Nova Web Technologies LLC; San Diego (CA); On-site; USD 62,000 - 103,000; Full time

Job summary

Nova Web Technologies LLC is seeking a Bioinformatics Pipeline Test Engineer in San Diego to validate and ensure the quality of NGS data pipelines and workflows. The role focuses on testing strategies, data validation, and automation using Python.

You will work with a cross-functional team to enhance pipeline reliability, support production testing, and integrate CI/CD practices in cloud-based environments. Candidates should have 2+ years of relevant experience and strong analytical skills.

Qualifications

• 2+ years in bioinformatics, genomics, data pipeline testing, or QA.
• Strong understanding of NGS workflows.
• Hands-on with FASTQ, BAM, VCF formats.
• Experience in pipeline QA and data testing.
• Strong Python scripting/automation.

Responsibilities

• Design and execute testing strategies for NGS pipelines, including alignment, variant calling, and annotation workflows.
• Perform data validation, regression testing, and discrepancy analysis across bioinformatics pipelines.
• Develop automated test scripts and validation utilities using Python.
• Translate requirements into test cases and validation criteria.
• Validate genomic data formats and processing workflows (FASTQ, BAM, VCF).
• Identify, document, troubleshoot, and track pipeline defects and data quality issues.
• Work with CI/CD pipelines and cloud-based data workflows to support testing and deployment.
• Collaborate with bioinformatics engineers, data engineers, developers, and QA teams to improve quality.
• Support testing of production and cloud-based data pipelines.

Skills

Bioinformatics testing

NGS workflows

Python scripting

Git

CI/CD

Cloud platforms (AWS/GCP/Azure)

Data validation

Troubleshooting

Communication

Tools

Nextflow

Snakemake

WDL/Cromwell

Job description

Position Overview

We are looking for a Bioinformatics Pipeline Test Engineer to validate and ensure the quality, accuracy, and reliability of NGS data pipelines and bioinformatics workflows.

Location

San Diego, CA

Experience

2+ Years

Employment Type

Contract

Key Responsibilities

• Design and execute testing strategies for NGS pipelines, including alignment, variant calling, and annotation workflows.
• Perform data validation, regression testing, and discrepancy analysis across bioinformatics pipelines.
• Develop automated test scripts and validation utilities using Python.
• Translate functional and technical requirements into comprehensive test cases and validation criteria.
• Validate genomic data formats and processing workflows, including FASTQ, BAM, and VCF.
• Identify, document, troubleshoot, and track pipeline defects and data quality issues.
• Work with CI/CD pipelines and cloud-based data workflows to support automated testing and deployment.
• Collaborate with bioinformatics engineers, data engineers, developers, and QA teams to improve pipeline quality and reliability.
• Support testing of production and cloud-based data pipelines and help troubleshoot issues across environments.

Must-Have Skills

• 2+ years of relevant experience in bioinformatics, genomics, data pipeline testing, or QA.
• Strong understanding of Next Generation Sequencing (NGS) workflows.
• Hands-on experience with FASTQ, BAM, and/or VCF data formats.
• Experience in bioinformatics pipeline testing, QA, validation, or data testing.
• Strong Python scripting/automation skills.
• Hands‑on experience with Git and CI/CD tools.
• Experience working with cloud platforms such as AWS, GCP, or Azure.
• Understanding of data pipelines and automated testing frameworks.
• Strong analytical, troubleshooting, and problem‑solving skills.
• Excellent communication and collaboration skills.

Preferred Qualifications

• Experience in the biotechnology, healthcare, genomics, or life sciences industry.
• Familiarity with workflow orchestration tools such as Nextflow, Snakemake, WDL, or Cromwell.
• Experience with variant calling and genomic data validation.
• Exposure to regulated environments such as FDA or CLIA.
• Experience working with cloud-based bioinformatics pipelines.
• Knowledge of reference/golden datasets for data validation.
• Experience with automated regression testing and pipeline validation.