Hey @MiriamGorostidi ,
Let me tell my experience on using Ion Torrent Sequences in DADA2, Well I had tried with trunc-len command and the results were terrible, only less% had passed the filter and I think it is better to used go with trunc-len as 0 along with trim-left 15. For further reference,please do this check this one.
Note - I had used single end sequences for the analysis. And I am not also an expert in this one so it may be different for other IT sequences.
- I think it depends upon the question you are asking but you can do both the methods or you can also do DADA2 ASV then use that sequences for the OTU clustering.
Best,
Sreevatshan.