search

marbl / merqury

k-mer based assembly evaluation
Other
272 stars 19 forks source link

even number k-mer size #110

Open hui-liu opened 10 months ago

hui-liu commented 10 months ago

Hi, I got the best k-mer size is 19.7 by best_k.sh, I wonder if it is correct to use the 20-mer as the k-mer size.

Thanks, Hui

arangrhie commented 9 months ago

Hello, take the ceiling number from best_k.sh. This is the minimum size of k, allowing certain collision in the kmer space. You could use larger k with recent, more accurate datasets. It doesn't matter being even or odd.

Best, Arang