Senior Bioinformatics Software Engineer – Pipeline Development (Remote, US)

OMG Technology • New Jersey City, NJ

1d • Remote

About The Position

We are seeking an experienced Senior Bioinformatics Software Engineer to design, develop, and maintain scalable, production-grade NGS bioinformatics pipelines supporting clinical diagnostics and genomic applications. The role focuses on pipeline development and orchestration with Nextflow and Seqera Platform, software development in Python, and deployment on AWS and AWS HealthOmics. The position is remote and offered as a C2C or W2 contract for an initial duration of six or more months, with a high possibility of extension.

The engineer will help transition research algorithms into production environments and ensure clinical-grade pipelines are reproducible, traceable, validated, reliable, and compliant with relevant clinical software standards. The work involves collaboration with bioinformatics scientists, R&D, DevOps, and clinical teams, as well as performance and cloud-cost optimization. The role contributes to cancer diagnostics and genomic applications using NGS technologies.

Requirements

• MS or PhD in Bioinformatics, Computer Science, Engineering, or a related field.
• 7+ years of relevant experience, including 5–8+ years in bioinformatics software engineering.
• Strong hands-on experience developing NGS analysis pipelines in production environments.
• Advanced proficiency in Python and software engineering best practices.
• Strong experience with Nextflow and Seqera Platform.
• Experience deploying and scaling bioinformatics workflows on AWS.
• Hands-on experience with Docker, Git, CI/CD, and automated testing.
• Experience developing software in regulated clinical environments (ISO 13485, IEC 62304, ISO 15189, or equivalent).
• Understanding of NGS assays, genomic data processing, and clinical diagnostics.

Nice To Haves

• Experience with DRAGEN, Sentieon, or similar NGS analysis tools.
• Hands-on experience with AWS HealthOmics.
• Knowledge of AWS EC2, Batch, S3, and Lambda.
• Experience with oncology genomics, liquid biopsy, or molecular diagnostics.
• Familiarity with Singularity and workflow performance optimization.

Responsibilities

• Design, develop, and optimize scalable NGS bioinformatics pipelines for clinical diagnostic applications.
• Build and maintain workflow orchestration using Nextflow and Seqera Platform.
• Develop production-ready bioinformatics software using advanced Python programming.
• Deploy, scale, and optimize genomic analysis pipelines on AWS and AWS HealthOmics.
• Implement containerized workflows using Docker and/or Singularity.
• Develop CI/CD pipelines, automated testing, regression testing, and controlled software releases.
• Ensure reproducibility, traceability, validation, and compliance with clinical software standards.
• Collaborate with bioinformatics scientists, R&D, DevOps, and clinical teams to transition research algorithms into production environments.
• Optimize pipeline performance, scalability, reliability, and cloud infrastructure costs.

Benefits

• Opportunity to work with cutting-edge NGS technologies and build scalable bioinformatics pipelines.
• Opportunity to contribute to innovative cancer diagnostics using Nextflow, Python, and AWS.
• Contract duration of 6+ months with a high possibility of extension.

What This Job Offers

• Career Level: Senior