Answers.Body: <p>I have seen the blasr aligner typically used for aligning PacBio reads to a reference.  Is there a reason why blasr would not be a good choice? I guess the very short sequence you are trying to align to might be an issue.  </p>
  
  <p>Minimap2 is capable of mapping pacbio reads, and can also do pairwise mapping to see if reads overlap with each other, so this function might help you:
  From <a href="https://github.com/lh3/minimap2" rel="nofollow noreferrer">https://github.com/lh3/minimap2</a></p>
  
  <pre><code>minimap2 -x ava-pb  reads.fq query_seq.fq &gt; ovlp.paf
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-25T13:38:15.323Z
Answers.LastActivityDate: 2019-09-25T13:38:15.323Z
Answers.UserDisplayName: Jay Moore
Body: <p>Very simple set-up: We have a PacBio long high-fidelity (HiFi) reads, genome sequencing, and some of those that contain a particular sequence. I want to find out which ones. The length of the query sequence is 7kb, though ideally I would use as query a sub-sequence of only 1.5kb.</p>
  
  <p>The output can the just the read ID or the full read sequence.</p>
  
  <p>We tried <a href="https://github.com/thegenemyers/DAMAPPER" rel="nofollow noreferrer">DAMAPPER</a> and it gives some decent results but it might not be appropriate to search for the shorter sub-sequence of 1.5kb. It also feels like an overkill for this purpose. </p>
  
  <p>Bear in mind that this is my first foray into long-read sequencing so my mindset is still very much one of short, low error-rate reads.</p>
  
Tags: <phylogenetics><pacbio>
Title: Best way to "fish" long reads that match a query sequence
ThreadText: # Best way to "fish" long reads that match a query sequence
  
  (Asked by: username_0 on 2019-09-25)
  
  Very simple set-up: We have a PacBio long high-fidelity (HiFi) reads, genome sequencing, and some of those that contain a particular sequence. I want to find out which ones. The length of the query sequence is 7kb, though ideally I would use as query a sub-sequence of only 1.5kb.
  
  The output can the just the read ID or the full read sequence.
  
  We tried [DAMAPPER](https://github.com/thegenemyers/DAMAPPER) and it gives some decent results but it might not be appropriate to search for the shorter sub-sequence of 1.5kb. It also feels like an overkill for this purpose.
  
  Bear in mind that this is my first foray into long-read sequencing so my mindset is still very much one of short, low error-rate reads.
  
  **Tags:** phylogenetics, pacbio
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-09-25. Score: 3 | Accepted answer
  
  I have seen the blasr aligner typically used for aligning PacBio reads to a reference. Is there a reason why blasr would not be a good choice? I guess the very short sequence you are trying to align to might be an issue.
  
  Minimap2 is capable of mapping pacbio reads, and can also do pairwise mapping to see if reads overlap with each other, so this function might help you:
  From <https://github.com/lh3/minimap2>
  
  ```
  minimap2 -x ava-pb  reads.fq query_seq.fq > ovlp.paf
  
  ```
  
  
  ---
  
  