DNA encoding
2-bit nucleotide encoding
Every nucleotide is encoded on 2 bits, most-significant-bit first within each word:
| Base | Encoding |
|---|---|
| A | 00 |
| C | 01 |
| G | 10 |
| T | 11 |
The Watson-Crick complement of a base is its bitwise NOT on 2 bits: \(\text{complement}(base) = \lnot base \mathbin{\&} \texttt{0b11}\).
Kmer encoding
A kmer of length \(k\) (\(k \le 31\)) fits in a single 64-bit word. The first nucleotide occupies the two most significant bits, each following nucleotide occupies the next two bits, and unused low-order bits are zero. Extracting nucleotide i (0-indexed from the 5′ end) is a shift-and-mask operation.
Reverse complement is computed by bit manipulation directly on the packed word, without any lookup table: complement every base, reverse the byte order, then reverse the order of 2-bit groups within each byte in two more passes, and finally realign the result to the most-significant bits.
Canonical form
The canonical form of a kmer is the lexicographic minimum of the kmer and its reverse complement:
Using the canonical form halves the kmer space and makes counting strand-independent: a kmer and its reverse complement are always treated as the same entity, regardless of which DNA strand was sequenced.