text: user425: 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.
  
  user37: I have used smalt a couple of times. Smalt is more flexible than bwa/bowtie and can be tuned to be more sensitive to divergent hits, which is useful to certain applications. I heard Sanger did evaluate a few mappers for some non-typical applications (not sure what). They found smalt to perform better. Also smalt was developed at Sanger. I guess they could modify smalt based on their needs, though I don't know the details.
  
original_text: 425: <p><a href="http://www.sanger.ac.uk/science/tools/smalt-0" rel="nofollow noreferrer">SMALT</a> seems to be one of the most used read mappers for bacterial data, see, e.g., <a href="https://scholar.google.com/scholar?q=%22smalt%22+bacteria&amp;as_ylo=2016" rel="nofollow noreferrer">this query</a>. 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. </p>
  
  <p>Could you name some of its distinguishing features (e.g., user support by Sanger Pathogens)? </p>
  
  <p>So far I have heard only arguments like "We use SMALT because everyone does it.", but this is not convincing enough for me.</p>
   37: <p>I have used smalt a couple of times. Smalt is more flexible than bwa/bowtie and can be tuned to be more sensitive to divergent hits, which is useful to certain applications. I heard Sanger did evaluate a few mappers for some non-typical applications (not sure what). They found smalt to perform better. Also smalt was developed at Sanger. I guess they could modify smalt based on their needs, though I don't know the details.</p>
  