Lead Bioinformatics Engineer

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

Benefits offered by this job

Health insurance

Well-being programs

Blueprint for Wellness

Mental health program

Vacation time

401(k) match

Stock purchase plan

Life insurance

Flexible Spending Accounts

Annual incentive

Education assistance

Career advancement

Job summary

Quest Diagnostics is seeking a Senior Bioinformatics Pipeline Engineer to design, architect, and scale clinical-grade NGS workflows in a hybrid Baltimore, MD area setting.

You will lead automated pipelines, collaborate with pathologists and software engineers, and ensure compliance with CAP/CLIA and FDA while optimizing cloud resources and implementing IaC and containerization.

Qualifications

• Proficiency in Python and Bash scripting.
• Extensive experience with Nextflow or Snakemake in high-throughput environments.
• Knowledge of BWA, GATK, DeepVariant, Mutect2, VEP, SnpEff and FASTQ/BAM/VCF formats.
• AWS cloud infrastructure experience (Batch, EC2, S3, IAM, CloudWatch).
• CI/CD and Git workflows, automation via GitHub Actions or Jenkins.
• Containerization with Docker and Singularity.

Responsibilities

• Architect, implement, and maintain scalable genomic pipelines for processing high-throughput clinical NGS data (WGS, WES, panels, RNA-Seq, etc).
• Develop, modularize, and optimize complex workflow code using Nextflow or Snakemake.
• Design and implement containerization strategies (Docker, Singularity) for isolation and portability.
• Lead migration, deployment, and monitoring of pipelines on cloud platforms (AWS).
• Drive SDLC best practices, CI/CD, testing, and comprehensive documentation.
• Profile, benchmark, and optimize cloud compute resources to reduce runtime and cost.
• Collaborate with pathologists, R&D scientists, and software engineers to integrate pipelines with LIMS and HL7/FHIR systems.
• Prepare Software Validation Plans and Validation Reports per CAP/CLIA, FDA, NYSDOH requirements.
• Establish automated regression testing and benchmark controls.
• Provide technical guidance and mentor junior engineers.

Skills

Python & Shell

Workflow Management

Genomic Tools

Cloud & DevOps

CI/CD & Git

Containerization

Education

Bachelor's in bioinformatics or related field

Master’s in bioinformatics or related field (preferred)

Tools

Docker

Singularity

AWS

Terraform

CloudFormation

Jenkins

GitHub Actions

Job description

Job Description

Pay Range: $130,000.00 - $160,000.00 / year

Salary offers are based on a wide range of factors including relevant skills, training, experience, education, and, where applicable, certifications obtained. Market and organizational factors are also considered. Successful candidates may be eligible to receive annual performance bonus compensation.

Benefits Information

• Day 1 Medical, supplemental health, dental & vision for FT employees who work 30+ hours


• Best-in-class well-being programs


• Annual, no-cost health assessment program Blueprint for Wellness®


• healthyMINDS mental health program


• Vacation and Health/Flex Time


• 6 Holidays plus 1 'MyDay' off


• FinFit financial coaching and services


• 401(k) pre-tax and/or Roth IRA with company match up to 5% after 12 months of service


• Employee stock purchase plan


• Life and disability insurance, plus buy-up option


• Flexible Spending Accounts


• Annual incentive plans


• Matching gifts program


• Education assistance through MyQuest for Education


• Career advancement opportunities


• and so much more!

We are a leading oncology diagnostics company dedicated to advancing precision medicine through cutting edge ultra-sensitive genomic technologies. As we expand our portfolio of minimal residual disease (MRD) testing solutions, we are seeking a highly skilled and motivated Senior Bioinformatics Engineer to join our team. This role offers the opportunity to contribute to the development and implementation of bioinformatics methods that directly impact cancer patient care, enabling improved monitoring, and more informed treatment decisions.

The Senior Bioinformatics Pipeline Engineer will design, architect, optimize, and scale our clinical-grade Next-Generation Sequencing Bioinformatics workflows.

As a senior technical contributor, you will bridge the gap between assay development, assay validation, and clinical informatics systems. You will lead the implementation of automated computational workflows that process massive genomic datasets, ensuring the rapid, accurate, and secure delivery of diagnostic insights. Operating within a regulated clinical laboratory environment, you will champion modern software engineering practices, Infrastructure as Code (IaC), containerization, and advanced cloud orchestration to ensure high reproducibility, robust security, and absolute compliance with CAP, CLIA, NYSDOH, and FDA regulations.

This professional will work in a hybrid capacity out of one of the following offices:

Baltimore, MD
Secaucus, NJ
Marlborough, MA
Lewisville, TX

Responsibilities

• Architect, implement, and maintain highly scalable genomic pipelines for processing high-throughput clinical NGS data (including Whole Genome, Whole Exome, Targeted Panels, RNA-Seq, Liquid Biopsy, and Somatic Variant Calling assays).


• Develop, modularize, and optimize complex workflow code using Nextflow or Snakemake to orchestrate data processing from raw sequencer output to final clinical variant interpretation.


• Design and implement containerization strategies (Docker, Singularity) to guarantee strict environment isolation, portability, and reproducibility across local HPC and cloud environments.


• Lead the migration, deployment, and monitoring of pipelines on cloud platforms (AWS), utilizing services such as AWS Batch, ECS, S3, Step Functions, Lambda, and CloudWatch.


• Drive the adoption of modern software development life cycle (SDLC) best practices, including Git branch strategies, continuous integration/continuous deployment (CI/CD) workflows, comprehensive automated unit/integration testing (pytest, linting), and structural code documentation.


• Profile, benchmark, and optimize cloud compute resources to systematically reduce runtime, improve data throughput, and control operational cloud spend.


• Collaborate closely with Molecular Pathologists, R&D Scientists, and Software Engineers to integrate genomic pipelines with Laboratory Information Management Systems (LIMS), local/cloud clinical databases (SQL/NoSQL), and electronic medical records via HL7/FHIR protocols.


• Author and execute formal Software Validation Plans, Software Design Specifications, Test Cases, and Validation Summary Reports in accordance with Quest's internal Quality System and regulatory frameworks (CAP/CLIA, FDA, NYSDOH).


• Establish automated regression testing frameworks, synthetic validation datasets, and benchmark controls to monitor pipeline precision, sensitivity, and clinical-grade accuracy.


• Provide technical guidance, conduct rigorous peer code reviews, and mentor mid-level and junior bioinformatics engineers on the team.

Qualifications

• Required Work Experience:
  
  
  
  • Python & Shell: Advanced proficiency in Python (including pandas, numpy, and testing libraries like pytest) and robust Bash/Shell scripting.
  
  
  • Workflow Management: Extensive hands-on experience designing and maintaining production-grade workflows using Nextflow (DSL2 preferred) or Snakemake in high-throughput environments.
  
  
  • Genomic Tools: Deep, working knowledge of NGS alignment, variant calling, and annotation suites (e.g., BWA, GATK, DeepVariant, Mutect2, VarDict, Ensembl VEP, SnpEff) and biological file formats (FASTQ, BAM, VCF, BED).
  
  
  • Cloud & DevOps: Demonstrated experience configuring and managing AWS cloud infrastructure (AWS Batch, EC2, S3, IAM, CloudWatch) using Infrastructure-as-Code (Terraform or CloudFormation).
  
  
  • CI/CD & Git: Strong expertise in git version control, collaboration (branching patterns, pull requests), and automation via GitHub Actions or Jenkins.
  
  
  • Containerization: Proficiency with Docker and Singularity, including multi-stage builds and optimization.
  
  
  
  


• Preferred Work Experience:
  
  
  
  • Regulated Environments: 2+ years of experience working in a clinical genomics space adhering to CAP, CLIA, GxP, or FDA Title 21 CFR Part 11 requirements.
  
  
  • LIMS & Integration: Experience integrating pipeline outputs into clinical reporting engines, relational databases (PostgreSQL, MySQL), or NoSQL databases.
  
  
  • Databases: Working knowledge of clinical genomics databases (e.g., ClinVar, gnomAD, COSMIC, ClinGen).
  
  
  
  


• Work Environment:
  
  
  
  • Hybrid work schedule
  
  
  
  


• Travel required


• Education
  
  
  
  • Required: Bachelor’s in bioinformatics, Computational Biology, Computer Science, Software Engineering, or a closely related quantitative field with 7+ years of professional industry experience.
  
  
  • Preferred: Master’s in bioinformatics, Computational Biology, Computer Science, Software Engineering, or a closely related quantitative field with 5+ years of professional industry experience with a strong track record of production-level pipeline development.
  
  
  
  

Quest Diagnostics honors our service members and encourages veterans to apply.

While we appreciate and value our staffing partners, we do not accept unsolicited resumes from agencies. Quest will not be responsible for paying agency fees for any individual as to whom an agency has sent an unsolicited resume.

Equal Opportunity Employer: Race/Color/Sex/Sexual Orientation/Gender Identity/Religion/National Origin/Disability/Vets or any other legally protected status.