Answers.Body: <p>When I've needed to do this, I use canu to assemble the nanopore reads (choosing the highest-quality reads that are at least half the length of the target), then map the assembled consensus back to the reference sequence.</p>
  <p>The Canu assembly part of that is described here:</p>
  <p><a href="https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-36wgq4n5yvk5?step=12" rel="nofollow noreferrer">https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-36wgq4n5yvk5?step=12</a></p>
  <p>There are numerous different ways to map the consensus assembled sequence to the reference sequence. <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome" rel="nofollow noreferrer">BLASTn</a> in &quot;align 2 or more sequences&quot; mode could be used, for example. Another option, because the sequences are relatively small and you're just aligning 2, is <a href="https://www.ebi.ac.uk/jdispatcher/psa/emboss_needle" rel="nofollow noreferrer">needle</a> from the EMBOSS suite.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-12T10:59:34.430Z
Answers.LastActivityDate: 2024-03-12T11:07:46.330Z
Answers.LastEditDate: 2024-03-12T11:07:46.330Z
Answers.UserDisplayName: gringer
Body: <p><em>This question was also asked on <a href="https://www.biostars.org/p/9589012/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>I received a set of Nanopore long reads of a ~3kbp long known plasmid with an unknown insert between 1kbp and 7kbp. Could you suggest a pipeline to assemble the reads and find the insertion?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-12T12:35:20.987Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <nanopore><long-reads>
Title: Finding insertion in a plasmid
ThreadText: # Finding insertion in a plasmid
  
  (Asked by: username_0 on 2024-03-12)
  
  *This question was also asked on [Biostars](https://www.biostars.org/p/9589012/)*
  
  I received a set of Nanopore long reads of a ~3kbp long known plasmid with an unknown insert between 1kbp and 7kbp. Could you suggest a pipeline to assemble the reads and find the insertion?
  
  **Tags:** nanopore, long-reads
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-03-12. Score: 2
  
  When I've needed to do this, I use canu to assemble the nanopore reads (choosing the highest-quality reads that are at least half the length of the target), then map the assembled consensus back to the reference sequence.
  
  The Canu assembly part of that is described here:
  
  <https://www.protocols.io/view/plasmid-sequence-analysis-from-long-reads-36wgq4n5yvk5?step=12>
  
  There are numerous different ways to map the consensus assembled sequence to the reference sequence. [BLASTn](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) in "align 2 or more sequences" mode could be used, for example. Another option, because the sequences are relatively small and you're just aligning 2, is [needle](https://www.ebi.ac.uk/jdispatcher/psa/emboss_needle) from the EMBOSS suite.
  
  
  ---
  
  