k-mer size

Question

k-mer size

TazinRahman1105050 opened this issue 2 years ago · 3 comments

TazinRahman1105050 commented 2 years ago

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

Answer 1 · 2022-07-27T06:18:04.000Z

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.

Answer 2 · 2022-07-27T18:24:19.000Z

Thanks for the clarification

Answer 3 · 2023-07-10T18:24:31.000Z

@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.