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:

\text{canonical}(kmer) = \min\big(kmer,\ \text{revcomp}(kmer)\big)

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.

DNA encoding

2-bit nucleotide encoding

Kmer encoding

Canonical form

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Theory

Kmer indexing

Phylogeny

Kmer-based

SNP-based

Usage

Formats