Spoligotype Mycobacterium Tuberculosis parameters

To run the tool, go to:

        Toolbox | Microbial Workflows (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | Spoligotype Mycobacterium Tuberculosis (Image type_spoligo1_16_n_p)

The tool takes sequence lists as input.

The tool will accept any reads, but as spoligotyping targets genomic regions in M. tuberculosis, you are unlikely to get meaningful results if the reads are not from the M. tuberculosis complex or its closely related strains. To avoid matching in off-target sequences, it is best practice to trim reads for adapters, quality, etc. In non-isolate samples it can also be beneficial to extract M. tuberculosis reads first e.g., by using Taxonomic Profiling before typing.

In the wizard, minimum coverage thresholds can be set (figure 10.1):

Image spoligoparam
Figure 10.1: Spoligotype Mycobacterium Tuberculosis parameters.

Both thresholds must be met for a spacer to be present. To apply only a count threshold, set the percentage to 0. Conversely, to apply only a percentage threshold, set the count to 1.