Answers.Body: <p>As recently <a href="https://twitter.com/aphillippy/status/1191821832891949056" rel="nofollow noreferrer">tweeted by A. Phillippy</a>, Canu v1.9 now supports HiFi reads. </p>
  
  <p>Therefore you should just read their manual and look for the implementation</p>
  
  <p>:)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-16T18:29:03.687Z
Answers.LastActivityDate: 2020-01-17T14:47:56.043Z
Answers.LastEditDate: 2020-01-17T14:47:56.043Z
Answers.UserDisplayName: Felipe Almeida
Answers.Body: <p>From the group of Heng Li there is <a href="https://github.com/chhylp123/hifiasm" rel="nofollow noreferrer">hifiasm</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-17T08:08:41.390Z
Answers.LastActivityDate: 2020-01-17T08:08:41.390Z
Answers.UserDisplayName: Wouter De Coster
Answers.Body: <p>The HiFi de novo assembly tool that <strong>PacBio</strong> has been developing is called <strong>IPA</strong>.</p>
  <p>It’s available on <a href="https://github.com/PacificBiosciences/pbipa" rel="nofollow noreferrer">pbbioconda</a> for command line use, and as a push-button pipeline in their SMRT Link software.</p>
  <p>I looked at a few examples of runtimes of <strong>IPA</strong> for different genome sizes:</p>
  <p>3 Gb human genome – ~600 CPU hours
  800 Mb complex plant – ~430 CPU hours
  400 Mb plant - ~100 CPU hours</p>
  <p><a href="https://github.com/chhylp123/hifiasm" rel="nofollow noreferrer">Hifiasm</a> seems to be more efficient as far as I can tell. In <a href="https://doi.org/10.1038/s41592-020-01056-5" rel="nofollow noreferrer">their paper</a> they have a few nice tables comparing it to HiCanu, Peregrine and Falcon.</p>
  <p><a href="https://i.sstatic.net/QCPit.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/QCPit.png" alt="enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-09-10T18:36:48.957Z
Answers.LastActivityDate: 2021-09-10T18:36:48.957Z
Answers.UserDisplayName: ilam engl
Body: <p>What assembler is appropriate for High-Fidelity PacBio reads?</p>
  
  <p>For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the error-correction step?</p>
  
Tags: <assembly><software-recommendation><long-reads><pacbio>
Title: What assembler is appropriate for High-Fidelity PacBio reads
ThreadText: # What assembler is appropriate for High-Fidelity PacBio reads
  
  (Asked by: username_0 on 2020-01-16)
  
  What assembler is appropriate for High-Fidelity PacBio reads?
  
  For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the error-correction step?
  
  **Tags:** assembly, software-recommendation, long-reads, pacbio
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2020-01-16. Score: 3
  
  As recently [tweeted by A. Phillippy](https://twitter.com/aphillippy/status/1191821832891949056), Canu v1.9 now supports HiFi reads.
  
  Therefore you should just read their manual and look for the implementation
  
  :)
  
  
  ---
  
  ### Answer by username_2 on 2020-01-17. Score: 2
  
  From the group of Heng Li there is [hifiasm](https://github.com/chhylp123/hifiasm).
  
  
  ---
  
  ### Answer by username_3 on 2021-09-10. Score: 1
  
  The HiFi de novo assembly tool that **PacBio** has been developing is called **IPA**.
  
  It’s available on [pbbioconda](https://github.com/PacificBiosciences/pbipa) for command line use, and as a push-button pipeline in their SMRT Link software.
  
  I looked at a few examples of runtimes of **IPA** for different genome sizes:
  
  3 Gb human genome – ~600 CPU hours
  800 Mb complex plant – ~430 CPU hours
  400 Mb plant - ~100 CPU hours
  
  [Hifiasm](https://github.com/chhylp123/hifiasm) seems to be more efficient as far as I can tell. In [their paper](https://doi.org/10.1038/s41592-020-01056-5) they have a few nice tables comparing it to HiCanu, Peregrine and Falcon.
  
  [![enter image description here](https://i.sstatic.net/QCPit.png)](https://i.sstatic.net/QCPit.png)
  
  
  ---
  
  