With the dramatic reduction in cost for next-generation sequencing, obtaining the complete genomic sequence of small pathogens such as bacteria and viruses is now affordable for many routine veterinary and herd health applications. The primary uses are currently source tracking and virulence typing. Source tracking is helpful in managing persistent issues on a farm such as Salmonella contamination on equipment or Listeria in bedding. It can also help to inform risks to personnel based on similarities to human strains, such as with rotavirus or Clostridium perfringens in calves. Monitoring of influenza D is also an emerging area. Virulence typing has immense potential to provide actionable clinical information based on functional genomics. In addition to serotype, virulence, and antimicrobial resistance prediction, the complete characterization of autogenous bacterins can aid in choosing the most appropriate strains and monitoring responses. Some of the current challenges are interpretation of results to practitioners and protection of confidentiality while contributing to open data initiatives to benefit researchers and public health.