Use cases for Flye vs LJA: only for HiFi reads?

[JohnUrban]

Hi all,

Thanks for the great tools as usual. I remember messing around with ABruijn way back, but haven't needed to do much more assembly until now. It appears that Flye replaced ABruijn (a while ago). It also appears like LJA, which has shared authors/developers, is aiming to replace Flye as long reads become more accurate in general. Is that interpretation true? If so, are there LJA parameters recommended for long reads other than HiFi?

Approaching that from a different angle, I have 10-20x coverage of ONT reads with an N50 of ~125 kb using the Ultra-Long Kit. I've basecalled using the "Super Accurate" mode with the GPU version of Guppy. Given that information, would you recommend using Flye or LJA? And with what parameters? Are there any other assemblers you think I should try?

Many thanks,

John Urban

[JohnUrban]

I got an answer to this question on the Flye Repo:
mikolmogorov/Flye#499

I will show myself out. :)