hello there. I know one base can be represented 2-bit, that means a 64-bits number maximal can represent a 32-mer. But if I want to represent a longer kmer, is there any more memory-efficient method.
Yes! The same trick that you can use with k <= 32 also works with longer k. The difference is just that the result doesn’t fit in a single machine word any longer, and so some of the bit-twiddling operations become a bit more complex. For example, most modern hardware supports 128-bit integers (and many modern languages, like Rust) expose this type natively. You can pack k <= 64 bits into a 128-bit integer.
Beyond that, or more generally, one typically uses an array of bytes of the minimum required size. Each byte is 8 bits and can hold 4, 2-bit encoded nucleotides. So if you need a 37-mer, say you could pack it into 10 bytes. Many tools have this type of capability. For example, you can take a look in the source code of KMC, or in the Kmer class from the Cuttlefish tool developed in my lab (e.g. here).
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Hi, rob, thanks to your reply and I wrote a demo in Rust. Repo here: https://github.com/dwpeng/kmer
Thank you for the detailed answer. I will read KMC' and cuttlefish's source code.