Quickmerge before or after haplotype purging for high heter rate plant assemblies?

[xiekunwhy]

Hi,

For a high heter rate (> 2%) plant genome, I got a hybrid assembly (BUSCO C ~84% D ~26%) and a ONT(~30X) alone assembly (BUSCO C ~80% D ~14%).

Should I need to remove redundance sequences before runing quickmerge ?

Best, Kun

[mahulchak]

Hi Kun,

It is better to remove the redundant sequences, although probably not necessary. Perhaps try it without removing them and see what happens. But removal of the redundant sequences will surely make things cleaner.

On Wed, Jun 3, 2020 at 7:56 PM xiekunwhy [email protected] wrote:

Hi,

For a high heter rate (> 2%) plant genome, I got a hybrid assembly (BUSCO C ~84% D ~26%) and a ONT(~30X) alone assembly (BUSCO C ~80% D ~14%).

Should I need to remove redundance sequences before runing quickmerge ?

Best, Kun

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