question about k-mer frequency

[XiaomingXu1995]

dear will-rowe,
HULK is concerned about the k-mer frequency as described in your paper. I find that a minimizer hash value cannot be added into the minimizerSketch when it is contained in the sketch(minimizer.go, line 195). So the hash values in the minimizerSketch are unique. We cannot add the same minimizer hash value into the minimizerSketch inside a window, but if two different windows have the same minimizer-kmer, shall we concern the k-mer frequency?

[will-rowe]

Hi @XiaomingXu1995 - you are right that only unique minimizers are added to a sketch for a read. It would be a good idea to take into account minimizer frequency, I should probably try that.

I'm afraid HULK has been neglected recently. I will do my best to get back to it and try some new ideas out, including your observation. Thank you for your interest in it.

[jianshu93]

Any update on this?

Thanks,

Jianshu

[will-rowe]

Hi Jianshu,

I'm afraid that I'm pushed for time at the moment and am unlikely to get to this anytime soon.

Will