Pavian is a web application for exploring classification results from metagenomics experiments. With Pavian, researchers can analyze, visualize, and transform results from various classifiers - such as Kraken, Centrifuge, and MethaPhlAn - using interactive data tables, heatmaps and Sankey flow diagrams. An interactive alignment coverage viewer can help in the validation of matches to a particular genome, which can be crucial when using metagenomics experiments for pathogen detection.