Viruses are an abundant biological entity on earth, and Uganda has been reported a hotspot for many viral infections. Emerging and re-emerging viral pathogens, have been attributed to various outbreaks that have claimed lives. Current diagnostic methods methods in Uganda such as PCR, immunologic assays and microarrays for detection and identificatiion of viral pathogens not only have a big turn around time, but are also limited in their ability to identify novel viruses. This has delayed diagnosis, led to mis-diagnosis and unproper prescription. Metagenomics sequencing and analysis has emerged as a possible diagnostic tool for viral pathogen detection and identification although it has not yet been adopted for epidemic investigations in Uganda. This research hypothesizes that application of metagenomics analysis in detection and identification of viral pathogens will enhance capacity of timely and accurate detection, thus improved viral disease surveillance and clinical diagnosis in Uganda. An easy-to-use pipeline for detection and identification of viral pathogens will be set up and applied to an actual metagenomics dataset. The results generated will inform and guide surveillance strategies for viral pathogens in Uganda.