Senior Bioinformatics Software Engineer

Job Title: Senior Bioinformatics Software Engineer – Pipeline Development

Location: Remote (USA)

Summary:

• The Senior Bioinformatics Software Engineer designs and delivers large-scale, clinical-grade bioinformatics platforms and pipelines supporting NGS diagnostic products.
• The role is accountable for production software used in regulated environments, with emphasis on performance, reproducibility, and release rigor.
• Specifically, the role supports Neo Genomics R&D in the development of new products and the improvement of existing ones by transforming R&D-level bioinformatics software into scalable, fast, robust, cost-effective, maintainable, regulated software suited to industrial-grade operations.
• The ideal candidate has demonstrated experience building and scaling workflow-driven systems using technologies such as DRAGEN, NetFlow, Seqera Platform, and AWS Health Omics.

Responsibilities:

Pipeline and platform engineering

• Design and implement scalable, clinical-grade NGS pipelines leveraging off-the-shelf and custom modules.
• Develop and scale bioinformatics algorithms and pipelines into production-ready, regulatory-compliant software products.
• Build and maintain workflow orchestration using Nextflow, with strong emphasis on reproducibility and observability.
• Develop and optimise bioinformatics workloads in cloud environments, including AWS and AWS Health Omics.
• Drive containerisation and environment reproducibility using Docker and/or Singularity.

Software development lifecycle

• Own components of the software development lifecycle, including architecture, implementation, testing, and controlled release.
• Implement robust CI/CD pipelines with automated regression testing and release validation for regulated software.
• Contribute to software quality management documentation and software testing to ensure developed systems conform to regulatory standards.
• Ensure auditability and traceability, and compliance with clinical software standards.
• Produce and adhere to proper validation documentation.

Collaboration and leadership

• Collaborate with algorithm and clinical teams to translate validated methods into production-grade software.
• Interface with R&D bioinformatics, database development, and DevOps teams for prioritisation and organisation of development work.

Information security and compliance

• Agree to abide by Employment and Confidentiality Agreements and End User Policies.
• Commit to staying up to date on training requirements for HIPAA/GDPR.
• Understand the importance of the proper handling and disposal of ePHI, and agree to follow HIPAA/GDPR regulations.
• Abide by the requirements for the proper disposal of equipment containing ePHI.
• Agree to report breaches and the improper handling of ePHI to the Company’s Privacy and Security Officers.

Education:

• MS or PhD in computer science, bioinformatics, engineering, or a related field, with industry-level bioinformatics software development or engineering experience and a proven track record.

Experience:

• Seven or more years of related experience; 5–8+ years of demonstrated experience in bioinformatics software engineering.

Essential

• Demonstrated experience developing and maintaining large-scale, production bioinformatics systems in clinical or regulated environments.
• Advanced-level Python development proficiency, including building testable, maintainable scientific software.
• Strong expertise in workflow frameworks such as Nextflow, with experience using Seqera Platform in production settings.
• Proven track record with development and optimisation for HPC/cloud platforms, including deploying and scaling pipelines in AWS.
• Proficiency in working with Docker.
• Experience with implementation and maintenance of NGS data analysis pipelines.
• Proven experience implementing CI/CD, automated testing, and controlled release processes.
• Proficiency in software versioning systems, e.g., Git, SVN.
• Prior experience developing software in a regulated environment (ISO 13485, EN/IEC 62304, ISO 15189, or other).
• Strong understanding of NGS assays (oncology preferred) and clinical-grade data processing requirements.

Desired

• Hands-on experience with DRAGEN, Sentieon, or equivalent high-performance NGS analysis platforms.
• Experience with AWS Health Omics or similar managed genomics platforms.
• Experience with AWS products, including EC2, Batch, S3, and Lambda.
• Proficiency in a compiled language, preferably C or C++.
• Experience with algorithm and systems design for parallel computing.
• Experience with Singularity or equivalent container runtimes.
• Proficiency in R.