comparing and aligning 2 de novo genomes

Question

[Len]

Hi,

Sorry, I am a bit of novice in that realm. I have two reference genomes from a single species that were generated by a third party (i.e., company). One is from a male and the other a female. However, when comparing their alignment, the order is off, ie, aligning the scaffolds doesn't work. I'm trying to correct the order of the male genome so that it aligns with the female's. Does anyone have any suggestions about pipeline or software to use?

Cheers, L

[samuel.a.odonnell]

What do you mean the order is off?

[Len]

Thanks for the reply.

What I meant is, for instance, one of the scaffolds in the female genome is broken into multiple scaffolds in the male genome. I aligned aligned both using minimap2, to look at order, but not I am trying to fix it so that the male genome is somewhat similar to that of the female. I hope this makes sense.

[samuel.a.odonnell]

Unfortunately it does not make much sense to me.. Maybe just post a dotplot of the chromosome alignment to show what you mean?