Next-generation sequencing is changing research methods in biological fields. Microbial identification and detection technologies based on next-generation sequencing have advantage of high-precision and radial-velocity need， and the capability to replace previous culture-based and molecular methods, such as using nucleic acid amplification and hybridization technologies for rapid response to known and unknown biological threats. In this paper, we compared current computational analysis approaches on next-generation sequencing data for microbial identification and detection, including design principles, computational pipeline, and benchmark testing. Furthermore, some possible problems were summarized involving the use of these computational approaches.