Hello, I plan to switch QIIME 1.9 to QIIME 2.0 and I am now learning QIIME 2.0 by myself. I have some questions/conceptions not very clear.
1>In Qiime 1.9, we normally use the concept of OTUs, which is most often used in publications. However, Qiime 2.0 introduced amplicon sequence variants (ASVs), which I have seen in the paper of DADA2. Are these two conceptions exchangeable (OTUs or ASVs)? If not, what is the difference between these two? Why Qiime 2.0 use ASVs instead of OTUs? I suppose ASVs would have some kind of advantages?
2>In Qiime 1.9, we have three different OTU picking methods? closed, open and denovo picking? By contrast, I didn’t see the Qiime 2.0 tutorial mentions any of these OTU picking methods. There are several tutorials online (moving pictures, fecal, etc.). All of them are used BLASTn methods, which is similar to pick_closed_OTUs.py? I am not sure if I am right? Does Qiime 2 support other OTU picking methods such as de novo and open? I saw a section called " Clustering sequences into OTUs using q2-vsearch", which seems a solution, but I am just confused why QIIME2.0 doesn’t use clustering as the default method.
3> In Qiime 1.9, the default OTUs clustering is 97% similarity level, which is very classical. However, I barely see Qiime 2.0 tutorial mention it. Most of tutorials used DADA2 workflow and quickly generated a feature table (OTU table) and corresponding feature sequences. So, we don’t do clustering in Qiime 2.0? If QIIME2.0 still does it, what is the default cut-off.
4>I am also very confused about the databases. All of the tutorial used BLAST against NCBI nt database. As you know, most of us just sequences 16S rRNA gene. In QIIME 1, we have RDP, Silvia and Greengenes, all of which are specific for 16S rRNA. As far as I know, NCBI nt database almost updated every week (it is very large) and I am not sure how QIIME2 could catch up the latest database? What is the default version of nt database in QIIME2? Also, BLAST is not very fast. I suppose it will be really slow if I have a very large sequencing data set. I remember there are several methods to annotate reads in Qiime 1.X (e.g., RDP, uclust, mothur etc.). Do you still support these methods?
Also, if I want to use greengenes or other databases, how I can do it?
5> After I generate a feature table, I can export it to biom format. However, there is no taxonomic name in this table. I can only see the taxa information by building a plot. I am not sure if I did this wrong. If I was correct, why QIIME2 remove the taxa information in the feature table.