A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and <i>In Silico</i> Approaches
Bert Bogaerts, Thomas Delcourt, Karine Soetaert, Samira Boarbi, Pieter‐Jan Ceyssens, Raf Winand, Julien Van Braekel, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Kathleen Marchal, Vanessa Mathys, Kevin Vanneste
Abstract
modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.