Answers.Body: <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>
  
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Answers.CreationDate: 2017-06-05T21:35:13.187Z
Answers.Text: 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.
Answers.UserDisplayName: Karel Břinda
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Answers.CreationDate: 2017-06-02T14:20:08.550Z
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Answers.UserDisplayName: user172818
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-01T15:16:47.883Z
Comments.Text: @user172818 Thank you!! This is exactly what I wanted to know.
Comments.UserDisplayName: Karel Břinda
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Comments.CreationDate: 2017-06-01T15:17:12.600Z
Comments.Text: Btw. What is interesting about the up/down-votes here is that whenever this question got 1 like, someone immediately put 1 dislike so the sum was 0 most of the time.
Comments.UserDisplayName: Karel Břinda
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Comments.CreationDate: 2017-06-02T07:46:33.077Z
Comments.Text: @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.
Comments.UserDisplayName: gringer
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Comments.CreationDate: 2017-06-04T18:02:53.907Z
Comments.Text: It is also recommended mapper for [reapr](http://www.sanger.ac.uk/science/tools/reapr), because it is able to align mate pairs independently to each other (`-x` option). I do not really know if other mappers do provide this option as well, I have not investigate that...
Comments.UserDisplayName: Kamil S Jaron
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Comments.CreationDate: 2017-05-31T14:09:09.623Z
Comments.Text: Is is really that popular? e.g. compare your query to this one: https://scholar.google.com/scholar?as_ylo=2016&q="Bowtie2"+bacteria I suggest you re-phrase to just ask about the differences between SMALT and the other algorithms
Comments.UserDisplayName: Chris_Rands
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Comments.CreationDate: 2017-05-31T14:17:14.383Z
Comments.Text: There are big clusters of researchers who do not use anything else than SMALT. For instance, a lot of people in bacterial population genomics.
Comments.UserDisplayName: Karel Břinda
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Comments.CreationDate: 2017-05-31T14:34:11.267Z
Comments.Text: Yes, or [this query](https://scholar.google.com/scholar?q=%22bwa%22+bacteria&btnG=&hl=en&as_sdt=0%2C5&as_ylo=2016). 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.
Comments.UserDisplayName: terdon
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Comments.CreationDate: 2017-05-31T14:39:43.113Z
Comments.Text: @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.
Comments.UserDisplayName: Karel Břinda
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T14:49:58.243Z
Comments.Text: Sure, counting google results is a horrible way of doing this. My point is that I don't see much evidence that this aligner is all that popular. I hadn't even heard of it, for example, and I've been working on NGS for the past couple of years and around people working on NGS for more than 15. I think you just happen to be in a community where this tool is over represented. I would have told you the *de facto* standard is BWA instead. I guess it just depends on what one has been exposed to.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T15:00:55.363Z
Comments.Text: I completely agree – I am now in a community where SMALT is highly overrepresented. I also consider BWA-MEM to be a standard (it is a little bit unfair for other mappers to talk about BWA as a whole since it comprises three distinct mappers). This is why I am trying find some reasons why SMALT is so popular in certain communities and to understand its distinguishing features from "more standard" mappers.
Comments.UserDisplayName: Karel Břinda
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-31T15:35:24.927Z
Comments.Text: Heh, I refer to BWA because where I work we've found that `bwa sampe` + `bwa samse` gives better results than `bwa mem` :)
Comments.UserDisplayName: terdon
Tags: <read-mapping>
Title: Why is SMALT better for microbial genomics than other mappers?
ThreadText: # Why is SMALT better for microbial genomics than other mappers?
  
  (Asked by: username_0 on 2017-05-31)
  
  [SMALT](http://www.sanger.ac.uk/science/tools/smalt-0) seems to be one of the most used read mappers for bacterial data, see, e.g., [this query](https://scholar.google.com/scholar?q=%22smalt%22+bacteria&as_ylo=2016). 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.
  
  **Tags:** read-mapping
  
  > **Comments:**
  > **username_3**: Is is really that popular? e.g. compare your query to this one: https://scholar.google.com/scholar?as_ylo=2016&q="Bowtie2"+bacteria I suggest you re-phrase to just ask about the differences between SMALT and the other algorithms  
  > **username_0**: There are big clusters of researchers who do not use anything else than SMALT. For instance, a lot of people in bacterial population genomics.  
  > **username_4**: Yes, or [this query](https://scholar.google.com/scholar?q=%22bwa%22+bacteria&btnG=&hl=en&as_sdt=0%2C5&as_ylo=2016). 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.  
  > **username_0**: @username_4 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.  
  > **username_4**: Sure, counting google results is a horrible way of doing this. My point is that I don't see much evidence that this aligner is all that popular. I hadn't even heard of it, for example, and I've been working on NGS for the past couple of years and around people working on NGS for more than 15. I think you just happen to be in a community where this tool is over represented. I would have told you the *de facto* standard is BWA instead. I guess it just depends on what one has been exposed to.  
  > **username_0**: I completely agree – I am now in a community where SMALT is highly overrepresented. I also consider BWA-MEM to be a standard (it is a little bit unfair for other mappers to talk about BWA as a whole since it comprises three distinct mappers). This is why I am trying find some reasons why SMALT is so popular in certain communities and to understand its distinguishing features from "more standard" mappers.  
  > **username_4**: Heh, I refer to BWA because where I work we've found that `bwa sampe` + `bwa samse` gives better results than `bwa mem` :)  
  > **username_0**: @username_5 Thank you!! This is exactly what I wanted to know.  
  > **username_0**: Btw. What is interesting about the up/down-votes here is that whenever this question got 1 like, someone immediately put 1 dislike so the sum was 0 most of the time.  
  > **username_1**: @username_5 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.  
  > **username_2**: It is also recommended mapper for [reapr](http://www.sanger.ac.uk/science/tools/reapr), because it is able to align mate pairs independently to each other (`-x` option). I do not really know if other mappers do provide this option as well, I have not investigate that...  
  
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  ## 1 answers
  
  ### Answer by username_5 on 2017-06-02. Score: 3 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: 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.  
  
  ---
  
  