For taxonomic assignment of eukaryotic metabarcoding datasets targeting the 18S gene, which reference database do you consider to be the best? My use case: mostly marine metazoans. SILVA and PR2 seem to be the big ones, whose respective philosophies seem to be quantity (SILVA) vs quality (PR2). PR2 was developed for marine protists initially, so I guess it may still have a bias in that direction. While SILVA on the other hand seems to include 18S sequences mainly just for microbial folks to be able to filter out eukaryotic contamination, with many of its annotations ending at Eukaryota. SILVA is much bigger though, but I don't know how big the overlap or difference in taxonomic focus is compared to PR2. Perhaps someone here can enlighten me? SILVA's choice to mix prokaryotic and eukaryotic sequences is of course beneficial also from a eukaryotic perspective, allowing filtering out prokaryotic contamination.
Then there's the option of merging and dereplicating the two databases, but in that case I would need advice on how to go about. But it would be really interesting if anyone has tried this and found an improvement.
