Senior Bioinformatics Pipeline Engineer — Hybrid

QUEST DIAGNOSTICS INC; Baltimore (MD); Hybrid; USD 130,000 - 160,000; Full time

Benefits offered by this job

Day 1 Medical

Dental & Vision

401(k) with company match

Employee stock purchase plan

Life and disability insurance

Flexible Spending Accounts

Annual incentive plans

Education assistance

Career advancement opportunities

Hybrid work schedule

Travel opportunities

Job summary

Quest Diagnostics Inc. is hiring a Senior Bioinformatics Pipeline Engineer to design, optimize, and scale clinical-grade NGS workflows. You will bridge assay development with informatics systems, implement automated pipelines, and ensure regulatory compliance in a hybrid work setting across multiple offices.

You will collaborate with pathologists and software engineers to deliver rapid, accurate diagnostic insights, emphasizing reproducibility, security, and cost efficiency.

Qualifications

• Advanced Python and Bash scripting skills.
• Experience designing production-grade workflows with Nextflow or Snakemake.
• Strong knowledge of genomic tools and file formats (FASTQ, BAM, VCF).
• Proven experience with AWS cloud infrastructure and IaC.
• CI/CD pipelines and Git collaboration.
• Containerization with Docker and Singularity.

Responsibilities

• Architect and maintain scalable clinical NGS pipelines.
• Develop and optimize workflow code for high-throughput data.
• Implement containerization for reproducible environments.
• Migrate and monitor pipelines on AWS using Batch, ECS, S3, and related services.
• Promote SDLC best practices, CI/CD, testing, and documentation.
• Guide and mentor junior engineers.

Skills

Python & Bash

Nextflow & Snakemake

NGS tools (BWA, GATK)

Cloud & DevOps (AWS)

CI/CD & Git

Docker & Singularity

Education

Bachelor’s in bioinformatics or related field

Master’s in bioinformatics or related field

Tools

Nextflow

Snakemake

AWS Batch

EC2 / S3

Terraform or CloudFormation

PostgreSQL / MySQL / NoSQL

Job description

Quest Diagnostics Inc. is hiring a Senior Bioinformatics Pipeline Engineer to design, optimize, and scale clinical-grade NGS workflows. You will bridge assay development with informatics systems, implement automated pipelines, and ensure regulatory compliance in a hybrid work setting across multiple offices.

You will collaborate with pathologists and software engineers to deliver rapid, accurate diagnostic insights, emphasizing reproducibility, security, and cost efficiency.