What would be an error model for PacBio HiFi reads?

Question

[sebastian.schmidt.helsinki]

Hi,

to evaluate genome assemblers I would like to simulate PacBio HiFi reads. However, there seems no read simulator available that has a HiFi mode (at least I did not find anything via Google. If someone can point me to something, it would be amazing.).

So I would just write my own simple read simulator for starters, and I was thinking about just adding random indels and subs with a 1% rate. This would roughly match the minimum Q20 that PacBio defines their HiFi reads as.

Is this a viable approach, or would I be missing some important characteristic?

Answer 1

[jean.elbers]

You could try something like I did here: https://github.com/chhylp123/hifiasm/issues/33

[sebastian.schmidt.helsinki]

Thanks, that looks good!