Answers.Body: <p>Assuming you're using long reads - and you really should if you're looking at highly-repetitive regions - try <a href="https://github.com/marbl/Winnowmap" rel="nofollow noreferrer">Winnowmap</a>, which has been used by T2T consortium members as a repeat-weighted mapper that performs better than minimap2.</p>
  <blockquote>
  <p>Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats.</p>
  </blockquote>
  <p>Also, use the CHM13 genome assembly (or the most recent telomere-to-telomere assembly available). It has lots of additional sequence compared to GRCh38, especially in repetitive regions.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-06-21T22:21:34.753Z
Answers.LastActivityDate: 2024-06-25T22:32:59.833Z
Answers.LastEditDate: 2024-06-25T22:32:59.833Z
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Body: <p>we are interested in detecting repetitive sequences in two cell lines, however, when performing the alignment with pbmm2 on GRCh38, not good results are obtained. We are trying to modify the parameters but no improvement is seen. Could you recommend any aligners which are suitable for aligning repetitive sequences?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-21T04:54:33.330Z
Comments.Text: This is a very good question. In theory its doable, but not sure anyone has done it.
Comments.UserDisplayName: M__
Tags: <long-reads><pacbio><human-genome>
Title: Aligners for repetitive sequences
ThreadText: # Aligners for repetitive sequences
  
  (Asked by: username_0 on 2024-06-20)
  
  we are interested in detecting repetitive sequences in two cell lines, however, when performing the alignment with pbmm2 on GRCh38, not good results are obtained. We are trying to modify the parameters but no improvement is seen. Could you recommend any aligners which are suitable for aligning repetitive sequences?
  
  **Tags:** long-reads, pacbio, human-genome
  
  > **Comments:**
  > **username_1**: This is a very good question. In theory its doable, but not sure anyone has done it.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2024-06-21. Score: 1
  
  Assuming you're using long reads - and you really should if you're looking at highly-repetitive regions - try [Winnowmap](https://github.com/marbl/Winnowmap), which has been used by T2T consortium members as a repeat-weighted mapper that performs better than minimap2.
  
  > Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats.
  
  Also, use the CHM13 genome assembly (or the most recent telomere-to-telomere assembly available). It has lots of additional sequence compared to GRCh38, especially in repetitive regions.
  
  
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