I'm studying a species where there is a reference genome that is assembled only at the scaffold level ("unplaced scaffolds"). See here https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Geospiza_fortis/101/.
My question is
- Do people generally treat a reference genome at the scaffold level as if each scaffold would be a chromosome?
- Should a scaffold vs chromosome level reference genome be treated differently?
- What are the main challenges for using a reference genome that is only at the scaffold level?
Basically, I often read in population genetics textbook that we have to study "chromosome". But I have a hard imagine, when having only scaffold, how the theory applies differently.