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Kmers.jl

Kmers.jl provides the Kmer <: BioSequence type which implement the concept of a k-mer, a biological sequence of exactly length k.

Compared to other BioSequences, Kmers are characterized by:

  • Being immutable bitstypes
  • Being parameterized by its length, such that the length can be known at compile time.

When kmers are short, and their length is known at compile time, these characteristics allow k-mers to be stack allocated, or stored in registers, allowing for much more efficient computation than arbitrary-length sequences.

Conceptually, one may use the following analogy:

  • BioSequence is like AbstractVector
  • LongSequence is like Vector
  • Kmer is like SVector from StaticArrays

Kmers.jl is tightly coupled to the BioSequences.jl package, and relies on its internals. Hence, you should expect strict compat bounds on BioSequences.jl.

Warning

Kmers are parameterized by their length. That means any operation on Kmers that change their length, such as push, pop, slicing, or masking (logical indexing) will be type unstable and hence slow and memory inefficient, unless you write your code in such as way that the compiler can use constant folding.

Kmers.jl is intended for high-performance computing. If you do not need the extra performance that register-stored sequences provide, you might consider using LongSequence from BioSequences.jl instead

Installation

You can install BioSequences from the julia REPL. Press ] to enter pkg mode, and enter the following:

pkg> add Kmers

If you are interested in the cutting edge of development, please check out the master branch to try new features before release.

Contributing

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

Take a look at the contributing files detailed contributor and maintainer guidelines, and code of conduct.

Questions?

If you have a question about contributing or using BioJulia software, come on over and chat to us on the Julia Slack workspace, or you can try the Bio category of the Julia discourse site.