ITS data from Ion torrant PGM

1

Dear all,
I would like to ask if any mothur workflow /SOPs suitable for ITS data generated with Ion Torrent PGM

Best,
Marwa

2

Hi Marwa,

Sorry, we don’t have anything and I don’t know of anything. I thought the IonTorrent reads would be much too short to sequence ITS data. Would it perhaps be better to use 2x250 MiSeq or PacBio sequencing?

pat

3

Thanks for your reply. Yes, Ion torrent gives short reads that is why I did sequence ITS1 region only and not the entire region.
So, I could not use mothur pipeline to analyze my data? I already did analyze my data using DADA2 pipeline and want to use other pipelines as a comparison study.

Best,
Marwa

4

People have certainly used mothur to analyze ITS data - but we don’t have a workflow for ITS like we do for 16S