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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Chromosemble: pseudochromosomes or superscaffolds #16

Closed fergsc closed 5 years ago

fergsc commented 5 years ago

Hi, I have used Chromosemble to scaffold an assembly with a related species genome. Whats the difference between pseudochromosomes and superscaffolds? Which should I use?

pseudochromosomes ended up with larger and fewer scaffolds. So I guess this is better, but is it accurate?

Thanks.

jonwright99 commented 5 years ago

It's likely that pseudochromosomes will be less accurate than superscaffolds as they have undergone more scaffolding. The only way you can determine accuracy is by comparison to existing datasets like genetic maps etc. In most genome assemblies you trade accuracy for scaffold length so which version you use will depend on what you want to do with the resultant assembly.

fergsc commented 5 years ago

Thanks, thats what I thought was happening. Becomes more a question about how closely related the scaffolding species is, or how similar the genomic structure of the two are.