Single-linkage Cluster analysis from iDNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

Clustering analysis of dereplicated metabarcoding Sequences to a curated reference database.

Metabarcoded sequences were concatenated with a reference database (Pipeline.txt; ecoPCRsequences.sh) for mammals in Berlin. pairwise distances of all sequences were calculated using Vsearch. Clusters were then built based on these distances (clusterFromPairs.py) with a threshold of 99% identity. An analysis of clusters (clusterAnalysis.py) was carried out to ensure that clusters contained sequences from samples and those from the database. Clusters formed from sequences from samples only are given a species assignment