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

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.

The ideal candidate will have strong hands-on experience with Nextflow, Seqera Platform, Python, AWS, Docker, and CI/CD, along with expertise in clinical-grade NGS pipeline development and regulated software environments.

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 contribute to innovative cancer diagnostics using Nextflow, Python, and AWS.

Originally posted on Himalayas