The overall goal of the EnvMetaGen project No 668981 is to expand the research and innovation potential of InBIO – Research network in Biodiversity and Evolutionary Biology - through the creation of an ERA Chair in Environmental Metagenomics. This field was selected as the focus of the ERA Chair, because Environmental DNA (eDNA) analysis is increasingly being used for biodiversity assessment, diet analysis, detection of rare or invasive species, population genetics and ecosystem functional analysis. In this context, the work plan of EnvMetaGen includes one work package dedicated to the Deployment of an eDNA Lab (WP4), which involves the training of InBIO researchers and technicians for implementing best practice protocols for the analysis of eDNA (Task 4.2). These protocols are essential to the development of research projects in association with business partners and other stakeholders in key application areas identified in the project, and thus to the strengthening of InBIO triple-helix initiatives (InBIO-Industry-Government; WP5). This report (Deliverable D4.5) builds upon previous ones (Deliverables D4.2-D4.4, respectively Ferreira et al. (2018), Egeter et al. (2018), Paupério et al. (2018)) and provides an overview of the processing protocols for DNA sequence data generated by next-gen platforms within EnvMetaGen-affiliated projects. Deliverables D4.2-D4.5 form a detailed account of the successful deployment of a fully functional eDNA lab under the EnvMetaGen project and provide a valuable resource for eDNA practitioners in all spheres of the triple-helix model. This development was made possible through the recruitment of the ERA Chair team (WP2), secondments and Junior Researcher exchanges through the collaboration with international networks (WP3), an enhancement of computational infrastructure at InBIO (WP4) and participation of team members in workshops and conferences (WP6).