Advances in sequencing technology have led to producing vast quantities of data at relatively low cost. With no limitations to the data being generated, a significant challenge remains to analyze huge data and interpret biological meaning. Computational biologists have developed numerous software tools and databases which continue to evolve with this rapidly advancing field. In this study, tools to resolve two different problems with metagenomic data computational methods have been developed. First is the taxonomic annotation of complex metagenomes, where a pipeline was developed to calculate abundances of bacterial across samples, which is computationally fast and accurate. The second is a real world problem related to marine biology where efforts are being made to understand how microbes alter coral health. These host tissue samples are made up of a complex mixture of organisms (host and microbial associates) and identifying proportion of bacteria or coral host genome is challenging. To address this issue, a pipeline has been developed to identify reads that align to bacterial-specific housekeeping genes. To test these methods, a sample-set of coral tissue sample collected from the southern Line Islands was used to investigate the relative abundance of bacterial virulence factors across coral-algal interfaces. It has been shown that microbial communities associated with the coral-algal interface are enriched with members closely related to known bacterial pathogens, therefore we hypothesized that the virulence factors (VF) encoded by these microbes affect the coral health. We compared virulence genes abundance at both coral-coral and coral-algal interactions.