Hi Everyone,
I am attempting to use Qiime 2 (version 2020.11) to pass ASV information into Ghost Tree. I am following this tutorial here: Q2-ghost-tree Plugin: Community Tutorial for Creating Hybrid-Gene Phylogenetic Trees. I have successfully created my ASV table and representative sequence file using DADA2 and I am now trying to move forward with getting my ASVs ready for Ghost Tree. According to the tutorial, my next step is to dereplicate my ASVs using vsearch (they link the steps to this page here https://docs.qiime2.org/2018.8/tutorials/otu-clustering/). This is where I have issues. Vsearch’s dereplicate-sequences command requires a SampleData[Sequences] artifact which is not an output of DADA2. How can I extract the sequence data from my ASV output such that it will fit into vsearch’s parameters? I have tried running the closed-reference-clustering vsearch commands on my repset of ASV sequences (the next step) without the dereplication and it purges most of my sequences (I begin with ~7,000 ASVs and end with ~750 OTUs, as opposed to a UPARSE clustered dataset from the same sequences which yields ~4,000 OTUs). The tutorial mentions that moving forward without dereplication is problematic for vsearch and Ghost Tree. Where am I going wrong with the vsearch dereplication? Is there a way to obtain a seqs.fna file from my ASVs to use in the vsearch dereplication? Thank you,