Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
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!
1 answer
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.
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