Senior Bioinformatics Software Engineer – Pipeline Development (Remote, US)
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 clinical-grade NGS pipeline development in regulated software environments, using technologies including Nextflow, Seqera Platform, Python, AWS, Docker, and CI/CD. This is a remote contracting role supporting a diagnostics and pharma services company. The contract is for 6+ months, with a high possibility of extension. The role offers the opportunity to build scalable bioinformatics pipelines and contribute to cancer diagnostics.
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.
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What This Job Offers
Career Level
Senior
