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.