explore other options how to identify heterozygous kmers about smudgeplot HOT 4 CLOSED

Drafted in c03a52b

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Dear KamilSJaron,
Am I right that in case of high heterozygosity (for instance, intensive genome reshuffling after allotetraploidization accompanied by TE activation) smudgeplot can give incorrect prediction regarding to the genome ploidy level? How to present data obtained with GenomeScope2.0 in this case? And another question is about the coverage level of such genome (10x is too low or enough for estimation of main genome parameters?)
Sincerely,
Kira.

from smudgeplot.

Hi Kira,

smudgeplot is a visualization technique that uses closely related kmer pairs as a proxy for heterozygous and potentially paralogous loci. For different biological cases the interpretations can be more or less tricky (which is also the reason why we were thinking of using different ways to define kmer pairs). If you have some strange smudgeplots, you can open a new issue and post them there. I can take a look.

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We are probably quite happy about this in the end

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