Reference Database Comparisons
To compare the effectiveness of the three reference databases, we
examined the total number of ASVs and taxonomic ranks identified using
each database. We also investigated differences in taxonomic assignment
between single direction ASVs (comprised of forward- and reverse-only
sequence reads) and merged ASVs (merged paired-end sequence reads).
Specifically, we compared the CRUX-12S database to the combined
database to determine how the inclusion of additional region-specific
reference barcodes improved taxonomic assignment of California Current
fish species from eDNA samples. Next, we compared taxonomic assignments
between the FishCARD California Current-specific 12S reference
database and the combined reference database to determine whether a
curated metabarcoding reference database specific to a regional fauna
performs better than a database that uses all available 12Sreference barcodes.