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mbhall88 / drprg

Drug Resistance Prediction with Reference Graphs
https://mbh.sh/drprg/
MIT License
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Run TBProfiler #10

Closed mbhall88 closed 1 year ago

mbhall88 commented 2 years ago

Run TBProfiler on the isolates we select from https://github.com/mbhall88/drprg-paper/issues/1

The first part of this will be making a TBProfiler panel from our panel so that we are using the same.

mbhall88 commented 2 years ago

Actually, an important question here is whether we use TBProfiler's built in catalogue...

From the mykrobe paper

In order to separate the impact of catalogue from the different genotyping processes applied by different methods, we modified ARIBA to use the same catalogue as Mykrobe, but for the other tools we used their in-built catalogues.

If we want to really understand how much the methodology impacts the performance though we should use the same catalogue right?

Instructions on how to build a custom TBProfiler catalogue are at https://jodyphelan.gitbook.io/tb-profiler/quickstart/mutation-library. The main pain point with this will be that TBProfiler wants the variants in hgvs nomenclature, so I will have to convert mykrobe's variant format to hgvs.

iqbal-lab commented 2 years ago

I think same catalogue, and WHO to boot, is fine surely

mbhall88 commented 2 years ago

Sorry, I'm actually a little confused by what you just said...Got lost in the English-to-Australian translation?

iqbal-lab commented 2 years ago

Sorry, I'm just suggesting you use the same catalogue for both tools. Since the Mykrobe catalogue includes the WHO panel, I expect reviewers will see that as a positive.

Running both tools with both Mykrobe and TB profiler panels would be technically interesting but I propose don't bother.