You don't need to be confused. You have internet access (obviously) there are much more easy information available than you actually need to understand that. Please put some effort to gain easily understandable knowledge about the topic.
You have to determine what your goals are about this. You can sequence isolated bacteria, complete samples, cell culture supernatants, etc. The sample type defines the methods that you can use. You can find some articles talking about specific concerns about your chosen sample type. The main concerns could be extraction methods, preparation of the sample for sequencing, sequencing platforms, software to use for assembly, alignment, phylogenetics, antibiotic resistance, virulence markers, etc.