Does calculating the compressed k-mers have a great impact on the QV value?

marbl / merqury

k-mer based assembly evaluation

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Does calculating the compressed k-mers have a great impact on the QV value? #107

Closed XXH123a closed 9 months ago

XXH123a commented 1 year ago

Dear Dr. Arang Rhie, I have the genome assembled by three generations of data and the second-generation data used for correction. Does calculating the compressed k-mers have a great impact on the QV value? Is it meaningful to use merqury to evaluate genome at chromosome level?

arangrhie commented 11 months ago

Hello,

Compressed kmers violates the error model assumption used in the QV estimates. I wouldn't use that. Please use the non-compressed kmers to collect the QV on the (non-compressed) assembly.

Thanks, Arang