Bioinformatics Pipeline Test Engineer
Katalyst CRO • San Diego, California, United States
**Role & seniority: ** Bioinformatics Test Engineer (QA/Test; level not specified)
**Location & work type: ** Not specified (implied hybrid/remote not stated)
**Stack/tools: **
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Languages: Python
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Version control / CI-CD: Git; CI/CD tools (e.g., GitHub Actions, GitLab, Azure DevOps)
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NGS data formats: FASTQ, BAM, VCF
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Workflow engines (nice-to-have): Nextflow, Snakemake (also mentions WDL/Cromwell)
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Cloud (required/used): AWS/GCP/Azure; S3 implied
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Testing keywords: regression testing, discrepancy analysis, golden/reference datasets
**Top 3 responsibilities: **
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Design/execute testing strategies for NGS pipelines (alignment, variant calling, annotation).
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Validate data outputs and run regression/discrepancy analysis (e.g., VCF/BAM correctness).
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Build automated Python test scripts and integrate with CI/CD + cloud-based workflows.
**Must-have skills: **
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Strong understanding of NGS workflows (FASTQ → BAM → VCF).
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Experience with bioinformatics pipeline testing/QA.
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Python scripting for automation.
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Git and CI/CD hands-on experience.
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Experience with cloud-based data pipelines (AWS/GCP/Azure).
**Nice-to-haves: **
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Nextflow/Snakemake (or similar) familiarity.
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Regulated environment exposure (CLIA/FDA).
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Bio/biotech domain experience; real-world/production pipeline experience.
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Variant calling + VCF validation depth.
**Neutral screening signals (implied): **
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Full Description
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.
