TBProfiler provides M. tuberculosis spoligotyping functionality, but this option is not currently used in the TBProfiler module in TheiaProk. The request is to turn on that option in TBProfiler and add an additional output column containing the resulting spoligotype call.
:books: Context
Spoligotyping is a method for detection and typing of M. tuberculosis. Originally, this method is based on polymerase chain reaction amplification of a highly polymorphic direct repeat locus in the M. tuberculosis genome, but can now be performed bioinformatically using next generation sequencing data. Providing this functionality to the public health community will be valuable in detecting causative bacteria and in providing epidemiologic information on strain identities, and implementing such a method in clinic settings would be useful in surveillance of tuberculosis transmission and in interventions to prevent further spread of this disease.
:chart_with_upwards_trend: Desired Behavior
Running TheiaProk with default settings and M. tuberculosis NGS data as input will produce an output column containing spoligotyping results as determined by TBProfiler.
:cool:
:pushpin: Explain the Request
TBProfiler provides M. tuberculosis spoligotyping functionality, but this option is not currently used in the TBProfiler module in TheiaProk. The request is to turn on that option in TBProfiler and add an additional output column containing the resulting spoligotype call.
:books: Context
Spoligotyping is a method for detection and typing of M. tuberculosis. Originally, this method is based on polymerase chain reaction amplification of a highly polymorphic direct repeat locus in the M. tuberculosis genome, but can now be performed bioinformatically using next generation sequencing data. Providing this functionality to the public health community will be valuable in detecting causative bacteria and in providing epidemiologic information on strain identities, and implementing such a method in clinic settings would be useful in surveillance of tuberculosis transmission and in interventions to prevent further spread of this disease.
:chart_with_upwards_trend: Desired Behavior
Running TheiaProk with default settings and M. tuberculosis NGS data as input will produce an output column containing spoligotyping results as determined by TBProfiler.
:information_source: Additional Information
https://github.com/jodyphelan/TBProfiler?tab=readme-ov-file#spoligotyping