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tbtAMR was developed to address the need for a data-driven and flexible solution to inferring DST for M. tuberculosis in a clinical and public health laboratory.
tbtAMR is a very simple idea - users are able to supply at a minimum a vcf file (annotated with snpEff) and either leverage a default mutational catalougue and criteria. Or provide their own catalogues and intepretative criteria in csv format. This means that there is no need for a developer to update logic or databases, which makes updates and therefore reverification much more straightforward and user-firendly in a CPHL setting. In addition, with additional dependencies, if required DST can also be reported from paired-end reads.
For detailed instructions for installation, basic usage and use of your own custom criteria check out the links on the right