Project Summary As greater understanding of the important role that the human microbiome plays in human health has unfolded it is increasingly recognized that there is a vast and uncharted group of viruses that have direct and important influence on the composi�on, dynamics, and func�on of these microbial communi�es, and thus on the health of the human host. Metagenome sequencing efforts and other high-throughput methodologies have opened the door to large- scale cataloguing and characteriza�on of free-living viruses and prophage, which are resident in their bacterial host genomes. However, the diversity and lack of knowledge about these viruses hampers our ability to understand their poten�al impact. Illumina�ng the region outside of our current knowledge, so-called ‘dark mater’, is necessary to be able to understand, monitor, control, and u�lize virus-community interac�ons to promote human health. We hypothesize that applica�on of established and newly developed pipelines using these and other tools will allow vastly improved iden�fica�on and characteriza�on of viral elements that are impac�ng human microbiome dynamics, and that providing improved tools for visualizing these predic�ons and the rela�onships between them will have a broad impact on the field. To address these gaps we will develop enhanced methods for detec�on of viral sequences using graph assemblies, build a sequence- and structure-based pipeline for characteriza�on of auxiliary genes carried by viruses, and provide novel and useful ways of visualizing this complex informa�on to allow greater insight from researchers in the field.