Question: Assembled genome a little larger than Kmergeneie prediction?
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gravatar for gerrychang1985
18 months ago by
gerrychang198510 wrote:

Hi, everyone.

I've recently assembled a plant genome. It looks fine, with a scaffold N50 of 850K, and scaffolds longer than 10K take 90% of the total length. But here comes the question: the assembled genome size is a little larger (230Mb)than kmergenie prediction (205Mb). I've checked the histogram fit of kmergenie, and it looks quite good.

In my experience, the result of Kmergenie is usually smaller than the old method (kmer_num/depth_peak) and the assembly size. Does anyone know which number is more accurate?

Thanks.

ADD COMMENTlink modified 18 months ago by Rohit1.3k • written 18 months ago by gerrychang198510
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gravatar for Rohit
18 months ago by
Rohit1.3k
European union
Rohit1.3k wrote:

It would be probably easier for you to check the actual genome size predicted from flow cytometry or other wet-lab analysis. Since you haven't mentioned your plant species, check this out -

http://data.kew.org/cvalues/

For animals - http://www.genomesize.com/search.php

ADD COMMENTlink written 18 months ago by Rohit1.3k
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