This protocol provides a method to predict phage community diversity using the algorithm PHACCS.Sequencing of viral communities often results in a high percent of unknown reads, largely due to our incomplete reference databases. To address this unknown factor of viromes, the algorithm PHACCS (PHAge Communities from Contig Spectra) was developed to predict virus community alpha diversity without the use of taxonomic references. Based on the methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome."mBio6.5 (2015): e01578-15.