k-mer size

[TazinRahman1105050]

Dear concerned,

What is the largest value of k-mer works for MashMap? According to the help doc, we can use k-mer size up to 16. But I was running mashmap for some other experiments and found that k-mer size 20 also works. Thanks in advance, Tazin

[cjain7]

Mashmap uses 32 bit integer to save hashed k-mers. K-mers longer than 16 length will still get mapped to 32 bit space, leading to some degeneracy.

[TazinRahman1105050]

Thanks for the clarification

[bkille]

@TazinRahman1105050

A year late here, but I wanted to let you know that k-mers are now mapped to the 64-bit space, so you can have larger k-mer sizes without needing to worry about degeneracy.