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

OMG Technology; Jersey City (NJ); Remote; USD 96,000 - 165,000; Full time

Job summary

OMG Technology is seeking a Senior Bioinformatics Software Engineer to design, develop, and maintain scalable NGS pipelines for clinical diagnostics. The role emphasizes production-grade software, Nextflow orchestration, and cloud deployment on AWS.

The candidate will collaborate with bioinformatics scientists, R&D, DevOps, and clinical teams to transition research algorithms into production environments, ensuring reproducibility and compliance with clinical standards.

Qualifications

• MS or PhD in Bioinformatics, CS, Engineering or related field.
• 7+ years of relevant experience, incl. 5–8+ years in bioinformatics software engineering.
• Proven track record building production-grade NGS pipelines.
• Advanced Python and software engineering practices.
• Strong Nextflow and Seqera Platform experience.
• Experience deploying scalable bioinformatics workflows on AWS.
• Hands-on with Docker, Git, CI/CD and automated testing.
• Experience in regulated clinical environments (ISO 13485, IEC 62304, ISO 15189, or equivalent).
• Understanding of NGS assays and clinical diagnostics.

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 Python.
• Deploy, scale, and optimize genomic analysis pipelines on AWS.
• Implement containerized workflows using Docker and Singularity.
• Develop CI/CD pipelines, automated testing, and controlled releases.
• Ensure reproducibility, traceability, validation, and compliance with clinical standards.
• Collaborate with bioinformatics scientists and clinical teams to productionize research algorithms.
• Optimize pipeline performance and cloud cost control.

Skills

Python

NGS pipelines

Production software

Remote collaboration

Education

MS/PhD in Bioinformatics or related field

Tools

Nextflow

Seqera Platform

AWS

Docker

Singularity

Git

CI/CD

Job description

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

We are looking to hire a candidate with the mentioned skill sets and experience for one of our clients within the diagnostics and pharma services company. This is contracting and REMOTE role.

Job Summary

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.

Key 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.

Required Qualifications

• 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.

Preferred Qualifications

• 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.

Other Job Details:

• Job Type: C2C or W2.
• Duration: 6+ months with high possibility of extension.
• Location: REMOTE.
• Interviews: Video interviews.
• Docs required: ID proof will be required.

Why Should You Apply?

Work with cutting edge NGS technologies, build scalable bioinformatics pipelines and contribute to innovative cancer diagnostics using Nextflow, Python and AWS. Chance to c ontribute to innovative cancer diagnostics using Nextflow, Python, and AWS.