Bioinformatics Pipeline Test Engineer: NGS QA & Automation

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

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.