There is no built-in reference dataset when using the dada2: assignTaxonomy and Addspecies tool. How can I solve this?
Hi gjc,
I have the same question, but have been able (I think) to correctly run dada2’s assignTaxonomy using the Silva v138 database that can be downloaded from the dada2 github (Taxonomic reference data). I am wondering if Galaxy will incorporate any of these as reference data sets.
Update! The references have been included at the UseGalaxy public servers for a few years now, so I thought I’d let people know on these older topics! Details → Search results for 'assigntaxonomy' - Galaxy Community Help
You also have the option of loading your own! Topics like this one cover some of the formatting you may want to apply, whether working with the tools in your primary Galaxy history or in an RStudio environment attached to your history. Details → Dada2 Taxonomy assignment: memory resources, reference data formatting, Rstudio