The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences. Existing computational tools are typically focused on either eukaryotic virus discovery or virome composition analysis but not both. Here we present VirusSeeker, a BLAST-based NGS data analysis pipeline designed for both purposes. VirusSeeker has been successfully applied in several previously published virome studies. Here we demonstrate the functionality of VirusSeeker in both novel virus discovery and virome composition analysis.