The poultry industry is mostly challenged due to the impact of pathogens hampering the business. Early detection and intervention are crucial to avoid any severe economic impact as an outbreak is usually followed by embargoes and trade restrictions in affected areas. It would take up to two weeks in order to detect a virus using traditional methods. We developed molecular-based PCR and RT-PCR tools to detect viruses within a few days. Additionally, we are utilizing next-generation sequencing technology to characterize local viral strains floating among backyard chickens in the Nepalese landscape. With the advent of genomics tools, we are able to characterize viral strain and its virulence along with potential epidemics. Using Next-Generation Sequencing we have developed the capability to characterize viruses irrespective of its strain and subtype. One such example is Influenza A virus which is very difficult to characterize due to lack of PCR based assay. Using Next-Generation Sequencing Influenza A virus along with Newcastle disease virus has been successfully characterized.