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.

  • $\begingroup$ Is is really that popular? e.g. compare your query to this one: scholar.google.com/… I suggest you re-phrase to just ask about the differences between SMALT and the other algorithms $\endgroup$ Commented May 31, 2017 at 14:09
  • $\begingroup$ There are big clusters of researchers who do not use anything else than SMALT. For instance, a lot of people in bacterial population genomics. $\endgroup$ Commented May 31, 2017 at 14:17
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    $\begingroup$ Yes, or this query. In fact, if we go by the results of the three queries, it looks like SMALT is an order of magnitude less common than either Bowtie or BWA. $\endgroup$
    – terdon
    Commented May 31, 2017 at 14:34
  • $\begingroup$ @terdon BWA-MEM has 617 results. SMALT 162. I agree that it is less but it is still a highly used mapper and in certain communities the dominant one. Your last query (BWA) has a lot of results like biological warfare agents, etc. $\endgroup$ Commented May 31, 2017 at 14:39
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    $\begingroup$ @user172818 could you please put your flexibility explanation in as an answer to this question; it seems more appropriate as an answer rather than a suggestion for improvements to the question. $\endgroup$
    – gringer
    Commented Jun 2, 2017 at 7:46

1 Answer 1


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.

  • $\begingroup$ Thank you for your answer. Btw, Do you known how SMALT compares to NovoAlign? My guess is that Novoalign could perform better, but I have no evidence for it. $\endgroup$ Commented Jun 5, 2017 at 21:35

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