COMBAT-TB Workbench

COMBAT-TB Workbench performs analysis and management of Mycobacterium tuberculosis whole genome sequencing (WGS) data to enable detection of drug resistance, assessment of genetic diversity, and analysis of transmission dynamics.

Key Features:

• Modular Workflow Execution: Integrates the Galaxy platform to execute modular, predefined workflows for M. tuberculosis WGS analysis and phylogenetic studies.
• Integrated Analysis Tools: Workflows incorporate Trimmomatic, snippy, snp-sites, snp-dists, TB-Profiler, tb_variant_filter, and TB Variant Report for read preprocessing, variant calling, SNP alignment processing, distance calculation, and resistance profiling.
• Docker-based Deployment: Encapsulates the IRIDA Platform, Galaxy workflows, MariaDB, and dependencies in Docker containers for reproducible deployment.
• Data Ingestion and Metadata Management: Supports data upload via the IRIDA uploader command-line tool and automatic updating of sample metadata from workflow outputs.
• IRIDA Integration and Plugins: Uses irida-wf-ga2xml adaptations and custom IRIDA plugins to interface with recent Galaxy versions and streamline workflow execution and data handling.

Scientific Applications:

• Drug Resistance Detection: Identifies mutations associated with drug resistance in M. tuberculosis genomes using variant calling and TB-Profiler.
• Genetic Diversity Studies: Characterizes within- and between-strain genetic variation through SNP analysis and alignment processing.
• Transmission Dynamics Analysis: Enables phylogenetic and SNP distance analyses to investigate transmission pathways and outbreak relationships.

Methodology:

Customized Galaxy workflows incorporate Trimmomatic, snippy, snp-sites, snp-dists, TB-Profiler, tb_variant_filter, and TB Variant Report; integration with IRIDA is implemented via irida-wf-ga2xml adaptations and custom IRIDA plugins; deployment uses Docker containers containing IRIDA, Galaxy, and MariaDB; data are uploaded via the IRIDA uploader and workflow outputs are used to update sample metadata.