Answers.Body: <p>BWT based algorithm is just a component of a full-pledge aligner. To that end, it is applicable to most alignment tasks. However, for long-read alignment and metagenomes, we don't often use BWT based algorithms as other methods are faster.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-20T18:43:37.180Z
Answers.LastActivityDate: 2019-11-20T18:43:37.180Z
Answers.UserDisplayName: user172818
Answers.Body: <p>Not sure about the algorithm itself but Heng Li wrote an article about the future of BWA when releasing minimap2. It gives helpful insights about the topic : <a href="https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa" rel="nofollow noreferrer">Heng Li's blog</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T18:25:16.990Z
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Answers.UserDisplayName: Paul Endymion
Answers.Body: <p>Surely you know that neither bwa nor bowtie by itself is splice-aware?</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-20T20:54:05.723Z
Answers.Text: This isn't a limitation of the BWT algorithm, e.g. tophat2 uses bowtie2
Answers.UserDisplayName: Chris_Rands
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Answers.CreationDate: 2019-11-20T20:34:17.043Z
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Body: <p>Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not suitable.</p>
  
Tags: <phylogenetics><bwa><bowtie2>
Title: Is BWT based aligner suitable for any types of alignment task?
ThreadText: # Is BWT based aligner suitable for any types of alignment task?
  
  (Asked by: username_0 on 2019-11-20)
  
  Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not suitable.
  
  **Tags:** phylogenetics, bwa, bowtie2
  
  
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  ## 3 answers
  
  ### Answer by username_1 on 2019-11-20. Score: 3
  
  BWT based algorithm is just a component of a full-pledge aligner. To that end, it is applicable to most alignment tasks. However, for long-read alignment and metagenomes, we don't often use BWT based algorithms as other methods are faster.
  
  
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  ### Answer by username_2 on 2019-11-21. Score: 1
  
  Not sure about the algorithm itself but Heng Li wrote an article about the future of BWA when releasing minimap2. It gives helpful insights about the topic : [Heng Li's blog](https://lh3.github.io/2018/04/02/minimap2-and-the-future-of-bwa)
  
  
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  ### Answer by username_3 on 2019-11-20. Score: 0
  
  Surely you know that neither bwa nor bowtie by itself is splice-aware?
  
  > **Comments:**
  > **username_4**: This isn't a limitation of the BWT algorithm, e.g. tophat2 uses bowtie2  
  
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