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

Peter van Heusden; Ziphozakhe Mashologu; Thoba Lose; Robin Warren; Alan Christoffels

doi:10.1128/msphere.00991-21

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

mSphere. 2022 Feb 23;7(1):e0099121. doi: 10.1128/msphere.00991-21. Epub 2022 Feb 9.

Authors

Peter van Heusden¹, Ziphozakhe Mashologu¹, Thoba Lose¹, Robin Warren², Alan Christoffels^{1

3}

Affiliations

¹ South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
² DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch Universitygrid.11956.3a, Cape Town, South Africa.
³ Africa Centres for Disease Control and Prevention, African Union Headquarters, Addis Ababa, Ethiopia.

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. These components are combined into a single easy-to-install application using Docker container technology. We implemented two workflows, for M. tuberculosis sample analysis and phylogeny, in Galaxy. Building our workflows involved updating some Galaxy tools (Trimmomatic, snippy, and snp-sites) and writing new Galaxy tools (snp-dists, TB-Profiler, tb_variant_filter, and TB Variant Report). The irida-wf-ga2xml tool was updated to be able to work with recent versions of Galaxy and was further developed into IRIDA plugins for both workflows. In the case of the M. tuberculosis sample analysis, an interface was added to update the metadata stored for each sequence sample with results gleaned from the Galaxy workflow output. Data can be loaded into the COMBAT-TB Workbench via the web interface or via the command line IRIDA uploader tool. The COMBAT-TB Workbench application deploys IRIDA, the COMBAT-TB IRIDA plugins, the MariaDB database, and Galaxy using Docker containers (https://github.com/COMBAT-TB/irida-galaxy-deploy). IMPORTANCE While the reduction in the cost of WGS is making sequencing more affordable in lower- and middle-income countries (LMICs), public health laboratories in these countries seldom have access to bioinformaticians and system support engineers adept at using the Linux command line and complex bioinformatics software. The COMBAT-TB Workbench provides an open-source, modular, easy-to-deploy and -use environment for managing and analyzing M. tuberculosis WGS data and thereby makes WGS usable in practice in the LMIC context.

Keywords: Mycobacterium tuberculosis; bioinformatics; multidrug resistance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods
Humans
Mycobacterium tuberculosis* / genetics
Software
Tuberculosis*
Workflow

Grants and funding

MRC_/Medical Research Council/United Kingdom