<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>

CC BY-SA 4.0
2020-01-16T18:29:03.687Z
2020-01-17T14:47:56.043Z
2020-01-17T14:47:56.043Z
Felipe Almeida
<p>From the group of Heng Li there is <a href="https://github.com/chhylp123/hifiasm" rel="nofollow noreferrer">hifiasm</a>.</p>

CC BY-SA 4.0
2020-01-17T08:08:41.390Z
2020-01-17T08:08:41.390Z
Wouter De Coster
<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>

CC BY-SA 4.0
2021-09-10T18:36:48.957Z
2021-09-10T18:36:48.957Z
ilam engl
<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>

<assembly><software-recommendation><long-reads><pacbio>
What assembler is appropriate for High-Fidelity PacBio reads
# 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

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## 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

:)


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### Answer by username_2 on 2020-01-17. Score: 2

From the group of Heng Li there is [hifiasm](https://github.com/chhylp123/hifiasm).


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### 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)


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