The combat-tb workbench: Making powerful Mycobacterium tuberculosis bioinformatics accessible

Abstract

Whole-genome sequencing (WGS) is a powerful method for detecting drug resistance, genetic diversity, and transmission dynamics of Mycobacterium tuberculosis. Implementation of WGS in public health microbiology laboratories is impeded by a lack of user-friendly, automated, and semiautomated pipelines. We present the COMBAT-TB Workbench, a modular, easy-to-install application that provides a web-based environment for Mycobacterium tuberculosis bioinformatics. The COMBAT-TB Workbench is built using two main software components: the IRIDA platform for its web-based user interface and data management capabilities and the Galaxy bioinformatics workflow platform for workflow execution.