Senior Bioinformatics Pipeline Architect

Quest Diagnostics; Baltimore (MD); Hybrid; USD 130,000 - 160,000; Full time

Benefits offered by this job

Health benefits package

401(k) with company match

Annual incentive plans

Career advancement opportunities

Job summary

Quest Diagnostics seeks a Senior Bioinformatics Pipeline Engineer to design, architect, and scale clinical-grade NGS workflows. You will bridge assay development and clinical informatics, delivering automated, reproducible pipelines in a regulated lab setting.

Hybrid role based in a major US office, requiring collaboration with Molecular Pathologists and Software Engineers to integrate with LIMS/EMR via HL7/FHIR. Strong cloud, containerization, and SDLC experience is essential.

Qualifications

• 7+ years in a clinical genomics or bioinformatics role.
• Strong Python and shell scripting with unit/integration testing.
• Deep knowledge of NGS tools and file formats (BWA, GATK, DeepVariant, FASTQ, BAM, VCF).

Responsibilities

• Architect, implement, and maintain scalable genomic pipelines for clinical NGS data.
• Develop modular workflows using Nextflow or Snakemake.
• Design containerization (Docker, Singularity) for portability and reproducibility.
• Migrate, deploy, and monitor pipelines on AWS (Batch, ECS, S3, Step Functions).
• Lead SDLC practices and CI/CD with automated tests and documentation.
• Collaborate with Pathologists, R&D, and Software Engineers to integrate with LIMS and HL7/FHIR.

Skills

Python & Shell

Data manipulation

CI/CD

Testing

Education

Bachelor’s in bioinformatics or related field

Master’s preferred

Tools

Nextflow

Snakemake

Docker

Singularity

AWS

Terraform/CloudFormation

Job description

Quest Diagnostics seeks a Senior Bioinformatics Pipeline Engineer to design, architect, and scale clinical-grade NGS workflows. You will bridge assay development and clinical informatics, delivering automated, reproducible pipelines in a regulated lab setting.

Hybrid role based in a major US office, requiring collaboration with Molecular Pathologists and Software Engineers to integrate with LIMS/EMR via HL7/FHIR. Strong cloud, containerization, and SDLC experience is essential.