SMALT seems to be one of the most used read mappers for bacterial data, see, e.g., this query. I do not say that it is not a great mapper, but I cannot easily see what are its main strengths compared to mappers such as BWA-MEM, Bowtie2, NovoAlign or GEM. Moreover, it is not even published.
Could you name some of its distinguishing features (e.g., user support by Sanger Pathogens)?
So far I have heard only arguments like "We use SMALT because everyone does it.", but this is not convincing enough for me.