FAQ

Why can kmers not be compared to biosequences?

It may be surprising that kmers cannot be compared to other biosequences:

julia> dna"TAG" == mer"TAG"d
ERROR: MethodError
[...]

In fact, this is implemented by a manually thrown MethodError; the generic case Base.:==(::BioSequence, ::BioSequence) is defined.

The reason for this is the consequence of the following limitations:

• isequal(x, y) implies hash(x) == hash(y)
• isequal(x, y) and x == y ought to be identical for well-defined elements (i.e. in the absence of missings and NaNs etc.)
• hash(::Kmer) must be absolutely maximally efficient

If kmers were to be comparable to BioSequence, then the hashing of BioSequence should follow Kmer, which practically speaking would mean that all biosequences would need to be recoded to Kmers before hashing.

Why isn't there an iterator of unambiguous, canonical kmers or spaced, canonical kmers?

Any iterator of nucleotide kmers can be made into a canonical kmer iterator by simply calling canonical on its output kers.

The CanonicalKmers iterator is special cased, because with a step size of 1, it is generally faster to build the next kmer by storing both the reverse and forward kmer, then creating the next kmer by prepending/append the next symbol.

However, with a larger step size, it becomes more efficient to build the forward kmer, then reverse-complement the whole kmer.

Why isn't there an iterator of skipmers/minimizers/k-min-mers, etc?

The concept of kmers have turned out to be remarkably flexible and useful in bioinformatics, and have spawned a neverending stream of variations. We simply can't implement them all.

However, see the section Building kmer replacements on how to implement them as a user of Kmers.jl yourself.