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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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best parameters to work with ONT reads #710

Open AzizHN opened 1 year ago

AzizHN commented 1 year ago

Hello,

As there is nothing mentioned in the manual or other issues, can you please share with me your experiences when running kraken2 on ONT reads. What is the best kmer-length, the minimizer length, the minimizer spaces, etc.

What I think logically, is that working with longer k-mers would be more specific to species rather than shorter k-mers. But I want to be sure of that and since I don't have any statistical arguments I would love to listen to your experiences.

Any information can be helpful.

Thanks in advance.

ArmandBester commented 10 months ago

Hi

You could maybe have look at this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9725748/pdf/nihms-1850516.pdf. Under long read classification.