2
$\begingroup$

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?

Improve this question
$\endgroup$

3 Answers 3

Reset to default
3
$\begingroup$

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

:)

Improve this answer
$\endgroup$
2
$\begingroup$

From the group of Heng Li there is hifiasm.

Improve this answer
$\endgroup$
1
$\begingroup$

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

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.