Questions regarding genome assembly levels and sequence naming for Cactus alignment

[Liuyj-l]

Dear Professor,

I am currently performing a Cactus whole-genome alignment using 19 species genomes, and I would like to ask a few methodological questions.

First, is it necessary for all genomes included in the Cactus alignment to be at the same assembly level? For example, should all assemblies be at the scaffold level, or is it acceptable to include a mixture of chromosome-level assemblies and scaffold-level assemblies in the same alignment?

Second, do all input genomes need to use a unified sequence naming convention (e.g., chromosome or scaffold IDs), or can different naming schemes be used without affecting the alignment?

Thank you very much for your time and advice.

Best regards,
Liuyj

[glennhickey]

Your input genomes can have different assembly quality and you don't need to use any naming convention.