Generating summary files
The results from numerous runs can be collated into one table using the following command:
This will automatically create a number of colled result files from all the individual result files in the result directory. If you would like to generate this file for a subset of the runs you can provide a list with the run sames using the --samples flag. The prefix for the output files is tbprofiler by default but this can be changed with the --prefix flag.
Writing your own summary scripts
The collate function extracts the drug-resistance mutations and lineage, however you may want to extract more features that are present in the individual json result files. I have created a little tutorial on how to do this here.
iTOL files
Several files are produced by the tb-profile collate function. Among these are several config files that can be used with iTOL to annotate phylogenetic trees. A small tree and config files have been placed in the example_data directory. To use navigate to the iTOL website and upload the tbprofiler.tree file using the upload button on the navigation bar. Once this has been uploaded you will be taken to a visualisation of the tree. To add the annotation, click on the '+' button on the lower right hand corner and select the iTOL config files. You should now see a figure similar to the one below. The following annotations are included:
Lineage
Drug resistance classes (Sensitive, drug-resistant, MDR, XDR)
Drug resistance calls for individual drugs, were filled circles represent resistance.
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