Abstract Amplicon sequencing is a powerful research method designed to explore and reveal the taxonomic composition of diverse microbial communities. By focusing on specific genetic regions, researchers can gain insights into the structure and function of these communities. Typically, ribosomal ribonucleic acid (rRNA) or ribosomal deoxyribonucleic acid (rDNA) is sequenced, with particular attention given to key marker genes. For bacteria and archaea, the 16S rRNA gene is commonly targeted; for eukaryotes, the 18S rRNA gene is used, while fungi are often studied through internal transcribed spacers (ITS) regions. These marker genes provide the genetic signatures necessary for identifying and categorizing the various organisms present within a sample.

About This Material This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom. ## Questions this will address - What are the different subworkflows of the MGnify amplicon pipeline, and what is the function of each in the overall analysis? - How are the various subworkflows of the MGnify amplicon pipeline executed on Galaxy using ENA data? - How can you adapt and run these subworkflows using your own sequence data? - How can the retrieved outputs be used for further downstream analysis? ## Learning Objectives - Quality control to filter low quality and too short reads - Classify OTUs to SSU, LSU, and ITS regions - Visualize taxonomic abundance using Krona pie charts - Create taxonomic abundance summary tables - prepare MAPseq outputs for further downstream analysis using ampvis2