Chapter 10 Assigning taxonomy

To assign taxonomy we will use a custom reference database containing fish sequences available for the MiFish-U amplicon region for species found in Lake Tanganyika and its broader catchment area.

taxa <- assignTaxonomy(seqtab.nochim, 
          "/pub14/tea/nsc206/NEOF/metabarcoding_workshop/taxonomy/MiFish_Reference_Database_taxonomy.fasta", 
          multithread=TRUE, verbose = T)

taxa.print <- taxa
rownames(taxa.print) <- NULL
head(taxa.print)

This displays the taxonomic assignment of the first six ASVs at taxonomic levels from kingdom to species. The second ASV has not been assigned to any taxon in the reference database. Of the other five, two have been assigned at the species level, two at the genus level and one at the family level.