Given the question I am assuming you are doing de novo assembly to generate contigs from short reads and then you want to map the contigs against some sort of reference sequence? You can certainly do that, but again, it really depends on the question you are asking and what you are trying to do. As well as the state of reference sequences for your organism, and the expected variability. Especially with bacteria if there is high inter-strain variability most people treat strains as independent and do de novo assembly on the bacterial genomes versus reference-based mapping. It is always a good idea to read lots of papers in your area of exploration to get an idea of what people ion your sub-field are typically doing. You might chose to do something completely different and unique, but you want to know what is typically being done in order to justify your choices. Whether it is to do something fairly standard and typical in the workflow, or something very different.