The rapid development of sequencing technologies has to led to an explosion of pathogen sequence data that are increasingly collected as part of routine surveillance or clinical diagnostics. In public health, sequence data is used to reconstruct the evolution of pathogens, anticipate future spread, and target interventions. In clinical settings whole genome sequences identify pathogens at the strain level, can be used to predict phenotypes such as drug resistance and virulence, and inform treatment by linking to closely related cases. While sequencing has become cheaper, the analysis of sequence data has become an important bottleneck. Deriving interpretable and actionable results for a large variety of pathogens - each with their own complexities - from continuously updated data is a daunting task and requires flexible bioinformatics workflows and dissemination platforms. Here, we review recent developments in real-time analysis of pathogen sequence data with a particular focus on visualization and integration of sequence and phenotypic data.