Can TB Profiler be used to profile sequencing data from NTM samples?

[harrismia]

Hi Jody,

We have data from NTM samples that we would like to profiler for drug resistance mutations and get information about lineage etc. Could TB Profiler be used for this ? I assume we would need to specify the reference genome and the SNP database.

 Thanks!

      Michael 

[jodyphelan]

Yes TB-Profiler can be used for this. You would just have to specify the reference/gff and databases as in https://github.com/jodyphelan/tbdb/. I am currently workin on a tool which will support calling of species https://github.com/jodyphelan/NTM-Profiler. This is still in the early phase of development but eventually preformatted libraries should feature there for the common NTMs.

[harrismia]

Thanks very much for the information! I will definitely check out NTM-Profiler and look into using TB Profiler for NTM with a custom tbdb and reference/gff.