Annotate Unplaced Scaffold with Chromosome Information

Question

[Trevor]

I have a genome that has been assembled to a scaffold level, and a chromosome level genome from a related species.

My desire is to annotate the scaffolds with chromosome information from the chromosome level assembly. My current plans are to do so via mummer alignment, labeling each scaffold with the chromosome number that it had the highest degree of homology with. This approach may inaccurately label some scaffolds owing to structural variation between the two species (ie translocation). In order to alleviate this error slightly, i've gathered a total of 6 chromosome level assemblies of related species which I plan to use to cross verify with.

Are there any pre-existing tools to do something like this? Is this entirely the wrong approach?

[cmdcolin]

I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assembly and look for signatures of misassemblies (false contig joins may look like sv deletions, insertions, inversions, etc)