The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

Area of Science:

• * Bioinformatics
• * Microbiology
• * Public Health

Background:

• * Whole-genome sequencing (WGS) is crucial for understanding Mycobacterium tuberculosis (Mtb) drug resistance, genetic diversity, and transmission.
• * Implementing WGS in public health labs is hindered by a lack of user-friendly, automated bioinformatics pipelines.
• * Lower- and middle-income countries (LMICs) often lack skilled bioinformaticians and system support for complex WGS analysis.

Purpose of the Study:

• * To present the COMBAT-TB Workbench, a modular, easy-to-install application for Mtb WGS data analysis.
• * To provide a web-based bioinformatics environment integrating IRIDA and Galaxy platforms.
• * To facilitate WGS data management and analysis in resource-limited settings.

Main Methods:

• * Developed the COMBAT-TB Workbench using Docker containers to combine the IRIDA and Galaxy platforms.
• * Implemented Mtb sample analysis and phylogeny workflows within Galaxy.
• * Updated existing Galaxy tools and created new ones for specific Mtb analyses.
• * Developed IRIDA plugins and updated the irida-wf-ga2xml tool for workflow integration.

Main Results:

• * Created a modular, easy-to-install application for Mtb WGS bioinformatics.
• * Integrated IRIDA for user interface/data management and Galaxy for workflow execution.
• * Implemented functional Mtb analysis and phylogeny workflows with updated and new tools.
• * Enabled metadata updates with workflow results and provided flexible data loading options.

Conclusions:

• * The COMBAT-TB Workbench simplifies Mtb WGS data analysis, making it practical for LMICs.
• * This open-source solution addresses the need for accessible bioinformatics tools in public health microbiology.
• * Empowers laboratories in LMICs to leverage WGS for tuberculosis control and research.