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TB drug resistance pipeline

Hello,

I am with a Public Health lab in USA. What would be a suitable program for finding drug resistance in TB that would be as precise as wet lab testing? I tried using CLC but it had contradictory results to our wet lab testing. Please assist. I would ideally like a command line tool that I can include into a WDL workflow. Thank you.

genomics workflow
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updated by Jody Phelan • Jody Phelan • written by Moneeb Bajwa • Moneeb Bajwa

The first link does not give >90% resistance detection for some drugs and the second link is outdated as the tool's website said it had to shutdown due to lack of funding.

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written by Moneeb Bajwa • Moneeb Bajwa

I'm a bit late, but thought I would add my comments (as one of the devs on the first link's software). Getting >90% sensitivity has proved quite difficult for some of the second line drugs. This could be due incomplete characterisation of the molecular mechanisms (SNPs, indels, etc) or potential difficulties/error with performing phenotypic testing.

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written by Jody Phelan • Jody Phelan

What would be a suitable program for finding drug resistance in TB that would be as precise as wet lab testing?

Considering the nature of the work that you do, which is regulated at government level, should this not be opened up as a discussion among your colleague laboratories? Even if such a program existed, I would hope that it were extensively tested and ultimately approved by the CDC. Excuse me if this is just part of ongoing research. Irrespective, I am not aware of any program

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written by Kevin Blighe Kevin Blighe

Thank you. Yes this was just an exploratory question for potential future pipelines.

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written by Moneeb Bajwa • Moneeb Bajwa

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