Answers.Body: <p><a href="https://github.com/lh3/minimap2" rel="nofollow noreferrer">Minimap2</a> attempts to solve a lot of problems that are not properly dealt with by other mapping software. It's written by the same author as BWA, but designed to deal with situations where the reference and query sequences are quite different (e.g. for noisy long reads).</p>
  
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Answers.CreationDate: 2018-03-22T03:50:03.770Z
Answers.Text: This is a great point, thanks! I've heard good things about this with PacBio reads
Answers.UserDisplayName: EB2127
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Answers.CreationDate: 2018-03-22T16:35:56.310Z
Answers.Text: I will also keep this question open for a few more days; this is a great answer though!
Answers.UserDisplayName: EB2127
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Answers.CreationDate: 2018-03-21T23:41:06.860Z
Answers.LastActivityDate: 2018-03-21T23:41:06.860Z
Answers.UserDisplayName: gringer
Body: <p>I have a set of experiments which should result in WGS reads with a high density of indels. </p>
  
  <p>Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in performance, but rather "better" in terms of dealing with the presence of many deletions/insertions.</p>
  
  <p>Options I know of:</p>
  
  <ul>
  <li><p><a href="https://github.com/lh3/bwa" rel="nofollow noreferrer">BWA</a>  (I think there are special settings whereby I could run bwa
  for this case, e.g. see <a href="http://blog.liheng.org/2014/12/10/bwa-mem-for-long-error-prone-reads" rel="nofollow noreferrer">this</a>)</p></li>
  <li><p><a href="https://github.com/BioInfoTools/BBMap" rel="nofollow noreferrer">BBMap</a> </p></li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-20T19:15:19.610Z
Comments.Text: try Stampy? ...
Comments.UserDisplayName: Chris_Rands
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Comments.CreationDate: 2018-03-20T20:30:08.990Z
Comments.Text: @Chris_Rands Have you seen this benchmarked against the others?
Comments.UserDisplayName: EB2127
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Comments.CreationDate: 2018-03-21T11:04:52.040Z
Comments.Text: Which platform do you use? The link about bwa mem is about ONT platform. And what kind of indels are you talking about, small ones?
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-03-22T03:50:30.643Z
Comments.Text: @b.nota Small indels, but a high density of these small indels
Comments.UserDisplayName: EB2127
Tags: <phylogenetics>
Title: Are there certain alignment methods/tools which perform better with a high density of indels?
ThreadText: # Are there certain alignment methods/tools which perform better with a high density of indels?
  
  (Asked by: username_0 on 2018-03-20)
  
  I have a set of experiments which should result in WGS reads with a high density of indels.
  
  Question: Are there certain alignment tools/methods which perform respectively "better" with these reads? I'm not very interested in performance, but rather "better" in terms of dealing with the presence of many deletions/insertions.
  
  Options I know of:
  
  * [BWA](https://github.com/lh3/bwa) (I think there are special settings whereby I could run bwa
    for this case, e.g. see [this](http://blog.liheng.org/2014/12/10/bwa-mem-for-long-error-prone-reads))
  * [BBMap](https://github.com/BioInfoTools/BBMap)
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: try Stampy? ...  
  > **username_0**: @username_1 Have you seen this benchmarked against the others?  
  > **username_2**: Which platform do you use? The link about bwa mem is about ONT platform. And what kind of indels are you talking about, small ones?  
  > **username_0**: @b.nota Small indels, but a high density of these small indels  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-03-21. Score: 4 | Accepted answer
  
  [Minimap2](https://github.com/lh3/minimap2) attempts to solve a lot of problems that are not properly dealt with by other mapping software. It's written by the same author as BWA, but designed to deal with situations where the reference and query sequences are quite different (e.g. for noisy long reads).
  
  > **Comments:**
  > **username_0**: This is a great point, thanks! I've heard good things about this with PacBio reads  
  > **username_0**: I will also keep this question open for a few more days; this is a great answer though!  
  
  ---
  
  