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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?

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As recently tweeted by A. Phillippy, Canu v1.9 now supports HiFi reads.

Therefore you should just read their manual and look for the implementation

:)

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From the group of Heng Li there is hifiasm.

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The HiFi de novo assembly tool that PacBio has been developing is called IPA.

It’s available on pbbioconda 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 seems to be more efficient as far as I can tell. In their paper they have a few nice tables comparing it to HiCanu, Peregrine and Falcon.

enter image description here

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