Containers in Bioinformatics: Applications, Practical Considerations, and Best Practices in Molecular Pathology

Area of Science:

• Bioinformatics
• Clinical Genomics
• Computational Biology

Background:

• Implementing bioinformatics resources for next-generation sequencing (NGS) clinical testing presents significant IT infrastructure challenges.
• Ensuring scalability, reproducibility, security, and resilience is critical for handling genetic and protected health information within existing infrastructures.

Purpose of the Study:

• To highlight the current state of container technology adoption in NGS bioinformatics.
• To provide recommended best practices for building and utilizing containers in clinical bioinformatics settings.
• To focus on optimizing scalability, performance, maintainability, and data security.

Main Methods:

• Review of container technology principles and applications in bioinformatics.
• Analysis of current practices and challenges in clinical NGS bioinformatics.
• Development of best practice recommendations for container implementation.

Main Results:

• Container technology provides an infrastructure-agnostic solution for developing reproducible and scalable NGS bioinformatics pipelines.
• Standardized container usage can enhance productivity, simplify resource maintenance, and aid regulatory compliance.
• Inconsistent container adoption poses risks to performance, security, and privacy of protected health information.

Conclusions:

• Containerization is essential for robust and compliant clinical bioinformatics.
• Adherence to best practices in container implementation is vital for maximizing benefits and mitigating risks.
• Further standardization is needed to ensure optimal and secure use of containers in clinical NGS workflows.