Real-time analysis and visualization of pathogen sequence data

摘要: The rapid development of sequencing technologies has to led an explosion pathogen sequence data that are increasingly collected as part routine surveillance or clinical diagnostics. In public health, is used reconstruct the evolution pathogens, anticipate future spread, and target interventions. settings, whole genome sequences identify pathogens at strain level, can be predict phenotypes such drug resistance virulence, inform treatment by linking closely related cases. However, vast majority only for specific narrow applications typing. Comprehensive analysis these could provide detailed insight into outbreak dynamics, but not routinely done since fast, robust, interpretable work-flows in place. Here, we review recent developments real-time with a particular focus on visualization integration phenotypic data.