For mapping and exploring communities of both micro- and macroorganisms, high throughput sequencing of environmental DNA has become a powerful approach. One approach is to sequence a selected PCR amplified marker to obtain information about the taxonomic composition (DNA metabarcoding). In this course, we will focus on this approach. The students will be introduced to important analytical bioinformatics approaches from processing of raw sequence data to establishment of the OTU/sample matrix and retrieval of taxonomic identity of the sequences. Further downstream analyses will also be introduced. Important themes will be (1) different sequencing techniques, (2) filtering and quality assessment of high throughput sequence data, (3) error correction and/or clustering of high throughput sequence data, and (4) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including evolutionary placement of short-read sequences onto backbone phylogenies. In this regard we will also focus on long-read metabarcoding. Applications of a wide suite of tools will be presented, including DADA2, SWARM and VSEARCH. There will also be a few guest lectures, focusing on specific topics such as long-read metabarcoding and decontamination. The course will be a mix of lectures and hands-on sessions.