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k-mer based assembly evaluation
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Handling of assembly gaps #113

Closed cabbagesofdoom closed 11 months ago

cabbagesofdoom commented 11 months ago

Hi, Apologies if I have missed this in the docs/paper, but how does Merqury handle assembly gaps? Are the N bases treated just like any other (and thus generate a set of kmers unique to the assembly), or are they excluded/ignored? Thanks! Rich

brianwalenz commented 11 months ago

They are poison - a kmer cannot include or span an N. In effect, it is as if the sequence was split at any block of Ns.

cabbagesofdoom commented 11 months ago

Thanks!