Taxon‐specific BLAST percent identity thresholds for identification of unknown sequences using metabarcoding Methods in Ecology and Evolution

The identification of organisms in environmental samples using metabarcoding relies on factors such as taxonomic assignment methods, genetic markers, reference databases and confidence thresholds for taxonomic assignment. Because lineages evolve at different rates, a global threshold (e.g. an unknown sequence is assigned to a species name using a 97% BLAST percent identity threshold) is likely not optimal for accurate taxonomic assignments across all taxa, but no study has systematically evaluated taxon-specific confidence thresholds. We developed taxon-specific confidence thresholds for marine eukaryotes to improve the performance of BLAST-based assignment methods.