Bioinformatics Pipeline Test Engineer (Healthcare)

Novasoft; San Diego (CA); On-site; USD 90,000 - 150,000; Part time

Job summary

Novasoft in San Diego, CA is seeking a Bioinformatics Pipeline Test Engineer to validate NGS data pipelines and workflows. You’ll design tests for alignment, variant calling, and annotation, automate with Python, and ensure data quality across CI/CD and cloud environments.

Ideal candidates have 2+ years in bioinformatics QA, hands-on with FASTQ/BAM/VCF, and familiarity with Nextflow or Snakemake. Join a collaborative team advancing production-quality genomics solutions.

Qualifications

• 2+ years of bioinformatics, genomics, data pipeline testing, or QA experience.
• Strong understanding of Next Generation Sequencing (NGS) workflows.
• Hands-on experience with FASTQ, BAM, and VCF formats.
• Experience with bioinformatics pipeline testing, QA, validation, or data testing.
• Proficient Python scripting/automation and basic Git/CI/CD skills.
• Experience with cloud platforms such as AWS, GCP, or Azure.

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.

Skills

Bioinformatics knowledge

Python scripting/automation

Data pipeline testing

QA practices

CI/CD

Cloud platforms

Tools

Git

CI/CD tools

Nextflow

Snakemake

WDL

Cromwell

Job description

Location:San Diego, CA
Experience:2+ Years
Employment Type:Contract

Position Overview:

We are looking for aBioinformatics Pipeline Test Engineerto validate and ensure the quality, accuracy, and reliability of NGS data pipelines and bioinformatics workflows.

The ideal candidate will have a strong combination ofbioinformatics/genomics knowledge, software testing, Python automation, and data pipeline experience. This role will involve testing NGS workflows, validating genomic data, identifying defects and discrepancies, and collaborating with engineering and cross-functional teams to ensure production-quality solutions.

Key Responsibilities:

• Design and execute testing strategies forNGS pipelines, including alignment, variant calling, and annotation workflows.
• Performdata validation, regression testing, and discrepancy analysisacross bioinformatics pipelines.
• Develop automated test scripts and validation utilities usingPython.
• Translate functional and technical requirements into comprehensive test cases and validation criteria.
• Validate genomic data formats and processing workflows, includingFASTQ, BAM, and VCF.
• Identify, document, troubleshoot, and track pipeline defects and data quality issues.
• Work withCI/CD pipelines and cloud-based data workflowsto 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 experiencein bioinformatics, genomics, data pipeline testing, or QA.
• Strong understanding ofNext Generation Sequencing (NGS)workflows.
• Hands-on experience withFASTQ, BAM, and/or VCFdata formats.
• Experience inbioinformatics pipeline testing, QA, validation, or data testing.
• StrongPython scripting/automationskills.
• Hands-on experience withGitand CI/CD tools.
• Experience working withcloud 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 thebiotechnology, healthcare, genomics, or life sciencesindustry.
• Familiarity with workflow orchestration tools such asNextflow, Snakemake, WDL, or Cromwell.
• Experience with variant calling and genomic data validation.
• Exposure to regulated environments such asFDA 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.