Issues related to the application of cactus in plant genome alignment?

[Yolanda1201]

Hello, I am building the MSA by term of Progressive Cactus and then ran into some genomic data preprocessing issues. If the cactus team could advise me, I would be very grateful!

Firstly, the quality of the reference genomes needed to construct the MSA is an issue, some reference genomes are scaffold and contig level, are such genomes recommended to be added to the alignment?

Second, plant genomes are ploidy diverse, and I note that the cactus team suggests splitting polyploid genomes into multiple diploid genomes. Chromosomal sequences are easy to divide into subgenomes, but there are many scaffold and contig sequences in the reference genome in addition to those assembled to the chromosome level, how can these sequences be split into appropriate reference genomes?
Or for such genome sequences that include chromosomes, scaffold and contig in a ref genome, can we keep only the chromosome sequences and remove the other sequences that are not mounted successfully?

Thank you for your interest and I would appreciate any advice you can give me. Thanks to the Cactus team for this efficient alignment tool.