Recently, chain termination sequencing methods have been replaced by more efficient next-generation sequencing (NGS) methods. For influenza A, NGS allows for deep sequencing to characterize virus populations, efficient complete genome sequencing, and a non-sequence-dependent method to identify viral variants. There are numerous approaches to preparing samples for NGS and subsequent data processing methods that can be applied to influenza A sequencing. This chapter provides a brief overview of the process of NGS for influenza A and some useful bioinformatics tools for developing an NGS workflow for influenza A viruses.