Question 1: what exactly is the uchime_ref model ?
I have a query, Q, and suspected parents A and B. Is the model, M, the chimeric sequence that UCHIME chooses following a few different alignment strategies (as explained in Fig 2 of the original UCHIME paper?
Question 2: I couldn't find an explanation of what exactly the model represents in Robert Edgar's UCHIME2 page; is it safe to say that the VSEARCH implementation of uchime_ref we see here in QIIME2 is based on R. Edgar's UCHIME2?
Question 3: Does abundance information matter for reference-based detection? From the VSEARCH manual about chimera detection options:
In de novo mode, input fasta file should present abundance annotations (i.e. a pattern [;]size=inte- ger[;] in the fasta header).
Thanks!