Hello, me again.
I got lot of help from forum. And now I made a alpha, beta diversity analysis and even PERMANOVA test! I really appreciate qiime developers.
All of a sudden, I had a question.
I have followed two different approaches using qiime2 to analyze my amplicon data (COI)
- denoise with dada2-> “ASV table” -> diversity metrics
- denoise with vsearch-> VSEARCH (97, 98, 99% thresholds) -> “OTU table” -> diversity metrics
Which way would be in principle the most appropriate? I understand ASVs concept is somewhat close to the 100% OTU clustering. And ASVs sequence is the exact sequence.
In contrast, OTU clustered sequences are the consensus seqs. So it might not be the exact biological sequence. I read a lot of papers says ASVs is more powerful than OTU.
And my coworker asks that if ASVs seqs are 100% OTU, could I make ASVs table by
vsearch(100%thresholds) -> OTU clustering -> diversity analysis?
here is brief.
I think ASVs are more appropriate than OTUs. What is your recommendation by making ASVs table. by Dada2? or by Vsearch? (I choose Dada2, but as there are many options, my coworker’s opinion is vsearch).