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fbreitwieser / krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
GNU General Public License v3.0
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Can't use k of 39 (must be <= 31) #160

Open ailtonpcf opened 8 months ago

ailtonpcf commented 8 months ago

Hey, I would like to try Krakenuniq with kmers longer than 31, however I get an error: Can't use k of 39 (must be <= 31)

Is that really true that I can't use bigger kmer values, or a bug?

Thanks in advance, Ailton.

salzberg commented 8 months ago

yes that's correct - Krakenuniq uses an array that can only hold values up to 2^31 and there are places in the code that would break if you used longer k-mers. (And yes, I know that there are 4^31 possible DNA sequences of length 31.) Changing this would require a major code rewrite. Btw with longer k-mers you lose sensitivity rather quickly.