Are scaffolds in published draft genomes always ordered?

Question

[Dracaena]

Hi all,

I am struggling with a question. These days more and more non-model organisms get draft genomes, consisting of many scaffolds and here is my question: are these scaffolds within de draft genome always ordered? It does not seem te be mentioned in some publications, or is ordering just implied when publishing a draft genome? I know that scaffolds can contain gaps between contigs, so I imagine that scaffolds can also be ordered, even when there are gaps between them.

Cheers

Answer 1

[harish]

Not necessarily. For ordering the scaffolds you'll need a lot of information including Physical and Genetic Maps, or a closer chromosomal scale assembly, Hi-C data etc.

These information can then be jointly used to then order the contigs/scaffolds to orient them.

[Dracaena]

Thank you for your answer!