Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?

Question

[Mark]

Hi,

I'm looking to build assemblies of 2 eukaryotic species our group believes are related species to an organism that has a T2T assembly. I found this paper on reference-based assembly (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1911-6), but it's from 2017 and so I'm wondering if there any updated strategies for performing an assembly in this fashion.

Any advice would be appreciated!

Answer 1

[shelkmike]

You can do a de novo assembly and then scaffold the contigs using a reference by RagTag (https://github.com/malonge/RagTag). However, I personally don't like this approach because there can be structural differences even between genomes of closely related species.