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:

We are proud to offer best-in-class benefits and programs to support employees and their families in living healthy, happy lives. Our pay and benefit plans have been designed to promote employee health in all respects – physical, financial, and developmental. Depending on whether it is a part-time or full-time position, some of the benefits offered may include:

· 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!

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

• 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.

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.