Demultiplexed raw reads of the 12S-V5 Illumina MiSeq metabarcoding library using the 2 X 150 chemistry kit. The metabarcoding contains sequences of ~110 bp from various vertebrate groups. The files contained include true samples, positive control and negative controls. The data contained in the files was assessed using the Python package FastQC, while processing and filtering were conducted using the R package dada2 for Amplicon Sequence Variants (ASVs) generation. Downstream analysis was performed using R package phyloseq and formatted for ecological analyses using additional R packages (e.g. vegan).