Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2?

[colinbrislawn (Colin J Brislawn)]

@Jen_S

Our Ion Torrent specific data has an average about .2% to our best which is about 30% across all runs.

Ouch!

Try increasing the trimming parameters to remove low quality starting and ending positions.

Also, just to check, are you using denoise-pyro? The PD-mouse tutorial uses Illumina data, which has different defaults than pyro data like Ion Torrent.

Colin