Entering edit mode
3.1 years ago
Moneeb Bajwa
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10
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.
See if these help:
https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0650-x
https://www.nature.com/articles/s41598-018-33731-1
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90% resistance detection for some drugs and the second link is outdated as the tool's website said it had to shutdown due to lack of funding.
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.
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
Thank you. Yes this was just an exploratory question for potential future pipelines.