Answers.Body: <p>Usually, if you have HiFi reads, there is no way you can improve the assembly with short reads. Not just that they don't have higher quality, but they also map a lot worse. People sometimes use short reads for genome profiling and QCing the whole thing using Merqury.</p>
  <p>Not sure if there is benchmarking published though.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-03-15T12:07:31.503Z
Answers.LastActivityDate: 2024-03-15T12:07:31.503Z
Answers.UserDisplayName: Kamil S Jaron
Body: <p>I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this kind of data? I wanted to use hifiasm which seems the gold standard and then nextpolish2 but I am wondering if using for example spades to do an hybrid assembly would lead to something better or worse?
  This question is only intended to see if someone did such benchmarking before or not.</p>
  <p>Best regards,</p>
  
Tags: <assembly><illumina><pacbio>
Title: Hybrid assembly versus polishing for hifi and illumina reads
ThreadText: # Hybrid assembly versus polishing for hifi and illumina reads
  
  (Asked by: username_0 on 2024-03-14)
  
  I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this kind of data? I wanted to use hifiasm which seems the gold standard and then nextpolish2 but I am wondering if using for example spades to do an hybrid assembly would lead to something better or worse?
  This question is only intended to see if someone did such benchmarking before or not.
  
  Best regards,
  
  **Tags:** assembly, illumina, pacbio
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-03-15. Score: 2 | Accepted answer
  
  Usually, if you have HiFi reads, there is no way you can improve the assembly with short reads. Not just that they don't have higher quality, but they also map a lot worse. People sometimes use short reads for genome profiling and QCing the whole thing using Merqury.
  
  Not sure if there is benchmarking published though.
  
  
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