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maickrau / ribotin

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Can ribotin be applied to tetraploid genomes? #11

Open xujialupaoli opened 3 months ago

xujialupaoli commented 3 months ago

Hello! Thank you for providing such a useful tool. I have an autotetraploid genome. Can I also use ribotin to assemble the rDNA region? In addition, my tetraploid genome cannot be assembled well using hifiasm and verkko. The size of the assembled genome is very different from the estimated size of the genome.

maickrau commented 3 months ago

Hi, I haven't tested it on tetraploids but in principle it should work. Note that the results will not distinguish which haplotype the morphs came from. So the results can tell you which morphs are present somewhere in the rDNA but not how the morphs are distributed between the haplotypes.

Since it's a non-human genome you will have to get a species-specific rDNA sequences so ribotin can find the rDNA reads. You can get those by for example finding the rDNA contigs in the hifiasm or verkko assemblies and inputing just those contigs with the -r parameter, or if you have some previous partial rDNA assemblies from the same species that should also work. Here it doesn't matter if the rDNA is very poorly assembled by hifiasm or verkko, as long as they managed to make at least some rDNA contigs.