This protocol provides methods for quality control of metagenomic data. Included is adapter trimming, quality trimming, decontamination, negative control removal, and pre-processing results. Based on the methods found in 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."\u00a0mBio\u00a06.5 (2015): e01578-15.