I have been using QIIME for microbial community analyses for the past 5-6 years! the QIIME community has taught quite a large deal about how to analyse and infer the community data! Their tutorials and debugging strategies always made life easier for biologists like me. I have definitely been a big fan of their project.

Having said that, QIIME2 has impressed me even more! the use of DADA2 to filder your data to be devoid of noisy sequence reads makes it so much easy to interpret you data better. It has never been easy and biologically comprehensible to filter out the chimeric sequences (which is almost always the case when we do PCRs). Never been a fan of “OTUs” either and ASVs are definitely a much better way to represent the members of the microbial community.

I have made a short tutorial on how to get from the sequence read data all the way to making “Krona plots” to represent the relative abundance of the different members in your amplicon dataset. This can be accessed from my GitHub page AmpliSeq