These DADA2-formatted training fasta files were derived from the Ribosomal Database Project's Training Set 18 and the 11.5 release of the RDP database. These fastas were generated by the following commands (using the dada2 R package version 1.19.1): ## The RDP trainset data was downloaded from: https://sourceforge.net/projects/rdp-classifier/files/RDP_Classifier_TrainingData/ path <- "~/Desktop/RDP/RDPClassifier_16S_trainsetNo18_rawtrainingdata" dada2:::makeTaxonomyFasta_RDP(file.path(path, "trainset18_062020.fa"), file.path(path, "trainset18_db_taxid.txt"), "~/tax/rdp_train_set_18.fa.gz") ## Download "ten_16s.100.fa" from Robert Edgar's taxonomy testing page: https://drive5.com/taxxi/doc/fasta_index.html dada2:::tax.check("~/tax/rdp_train_set_18.fa.gz", "~/Desktop/ten_16s.100.fa") ## This function creates the dada2 assignSpecies fasta file for the RDP from the RDP's _Bacteria_unaligned.fa file. dada2:::makeSpeciesFasta_RDP("~/Desktop/RDP/current_Bacteria_unaligned.fa", "~/tax/rdp_species_assignment_18.fa.gz") dada2:::tax.check("~/tax/rdp_species_assignment_18.fa.gz", "~/Desktop/ten_16s.100.fa", mode="species")