2.5 Bioinformatic processing – metabarcoding
Reads were analyzed separately for each primer in R v 4.3.1 (R Core Team, 2023) using RStudio 2023.12.1 (RStudio Team, 2023) in dada2 (Callahan et al . 2016), after filtering (maxEE = 2, Q-scores Error model calculation, read correction, and read merging and removal of chimeric sequences was performed using default settings. Amplicon sequence variants (ASVs) identified by dada2 were assigned to taxa of origin using BLAST+ (v.2.6.0) (Altschul et al., 1990) and the GenBank database.