Sequences for eDNA tutorial

In this practical session, we will work with an eDNA metabarcoding dataset generated from coastal water samples collected across contrasting habitats in the Gazi Bay seascape, including reef, seagrass, mangrove-associated and open-water environments. The dataset contains MiFish/12S amplicon reads, which we will process through a simplified DADA2 workflow: inspecting raw reads, filtering and denoising them into ASVs, removing chimeras, assigning taxonomy using an instructor-curated fish reference database, and then asking what the recovered fish signal tells us about biodiversity across habitats. Our aim is not to exhaust every possible analytical choice, but to understand the logic of an eDNA bioinformatics workflow — how raw sequences become biological observations, how taxonomic confidence is evaluated, and how simple ecological plots such as richness, diversity, ordination, heatmaps and shared-taxa summaries can help us interpret whether water samples reveal structured fish communities across the seascape.