TBProfiler on amplicon data

[tianacs]

Hi Jody,

I'm interested in analysing TB amplicon sequencing data with TBProfiler and was wondering if it's suitable for that purpose? Have you considered using amplicon data before and do you have any recommendations and/or concerns?

[jodyphelan]

Hi @tianacs

It should work ok to use. The only thing is that the coverage report in the results won't make much sense as it will look at the entire gene rather than the amplicons. You can actually give your primers during database creation and it will then analyse just the amplicons instead of whole genes.

Let me know how it goes or if you have more questions.

[tianacs]

Ok, thank you. I'll give it a try and will follow up with questions

[jodyphelan]

Sure! Also forgot to mention, if you are using the ONT platform I would suggest using --caller bcftools