# Request for comments: Upcoming Kmers.jl version 1.0

**URL:** <https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203>\
**Category:** Biology, Health, and Medicine\
**Created:** [December 31, 2023, 10:02am UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203 "2023-12-31T10:02:44Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![jakobnissen](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jakobnissen/32/13477_2.png) [@jakobnissen](https://discourse.julialang.org/u/jakobnissen)\
**Post date:** [December 31, 2023, 10:02am UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203/1 "2023-12-31T10:02:44Z")

</div>

Dear BioJulia users and stakeholders,

I’m pleased to announce a preview of the first stable release of Kmers.jl, namely version 1.0.  
The release is essentially done and just needs some more testing and polishing, but before the release, I’d like feedback from potential users, and BioJulia stakeholders.  
This includes the original author of Kmers.jl, @Ward9250 and @kevbonham.

I’m especially interested in feedback regarding broader design issues: The API, issues with user experience of the package, scope etc.  
You can test it out by installing from the following branch: [https://github.com/BioJulia/Kmers.jl/pull/35](https://github.com/BioJulia/Kmers.jl/pull/35) . Note that you need to `dev` a compatible version of BioSequences.jl which is not yet released, but which can be found on this branch: [WIP: Kmers.jl compatibility by jakobnissen · Pull Request #282 · BioJulia/BioSequences.jl · GitHub](https://github.com/BioJulia/BioSequences.jl/pull/282)

## What is Kmers.jl?

Kmers.jl implements the `Kmer` type - this is a subtype of `BioSequence` which is immutable, a bitstype, and which has its length as a type parameter. These properties allows `Kmer`s to be stored in registers, allowing for much more efficient code than the generic `LongSequence` of BioSequences.jl.

As an analogy, if the types `BioSequence` and `LongSequence` from BioSequences.jl correspond to `AbstractVector` and `Vector`, then `Kmer` is `SVector` from StaticArrays.jl.

In bioinformatics, a kmer is a polymer molecule (typically DNA, RNA or peptide) consisting of exactly `k` linked molecules.  
In bioinformatics software, kmers are broadly used precisely for the performance characteristics of their implementation.

In Kmers.jl, performance is a top priority, and the methods are microoptimised to the best of my ability. For example, the following function creates a copy of the sequence that is reversed and complemented, and then picks the smaller of the two - it’s fully inlined and branchless:

```julia-auto
julia> @code_native debuginfo=:none dump_module=false canonical(mer"UGCUGUA"r)
        .text
        push rbp
        mov rbp, rsp
        mov rax, qword ptr [r13 + 16]
        mov rax, qword ptr [rax + 16]
        mov rax, qword ptr [rax]
        mov rcx, qword ptr [rdi]
        mov eax, ecx
        not eax
        mov edx, eax
        and eax, 13107
        shr edx, 2
        and edx, 819
        lea rax, [rdx + 4*rax]
        mov rdx, rax
        shl eax, 4
        shr rdx, 4
        and eax, 61680
        and edx, 3087
        or rax, rdx
        bswap rax
        shr rax, 50
        cmp rcx, rax
        cmovb rax, rcx
        pop rbp
        ret
        nop word ptr cs:[rax + rax]

```

## Design decisions

- A `Kmer` is an ordinary `BioSequence` - it is constructed like, and behaves as any other `BioSequence`.
- Performance is paramount. We’ll sacrifice precompilability, size of generated code, ease of use, and to some extent, latency, for performance.
- We are not going to implement different variations of the kmer concept, such as minimizers, k-min-mers and skipmers. These can be implemented in terms of the basic `Kmer` by users, if desired.
- Kmers.jl are for high performance code, meaning it’s aimed at somewhat experienced Julia users, so Kmers.jl is designed less for beginner programmers. For most use cases, BioSequences.jl will be good enough.

## A brief history of Kmers.jl

Before version 3 of BioSequences.jl was released about two years ago, BioSequences.jl contained a kmer type. However, we (Sabrina Ward and I) considered the old kmer type insufficient, as it had the following two limitations:

- It only supported the `Alphabets` `DNAAlphabet{2}` and `RNAAlphabet{2}`
- It only supported lengths up to 32 (with a `BigMer` type supporting length 64), insufficient for many use cases

To solve these issues, we created [two different](https://github.com/jakobnissen/experimental_kmer), repositories with [experimental implementations](https://github.com/BioJulia/NTupleKmers.jl), before settling on kmers backed by bits packed into `NTuple`s of integers.

We judged this new, more complex and specialized implementation should be moved out of BioSequences.jl for the breaking v3.0.0 release. When BioSequences.jl v3.0.0 was released in 2022, Kmers.jl was almost finished and would be released imminently… or so we thought.

In reality, development had stopped, and soon after, the author of Kmers, Sabrina Ward had to retreat from BioJulia development altogether which left Kmers.jl stillborn.  
This placed BioJulia in the awkward situation of having removed its only kmer implementation in 2022 in a breaking change, with nothing to replace it with.

After having been busy with [other BioJulia stuff](https://discourse.julialang.org/t/announcement-automa-v1-0-beta-preview/95753), I’ve recently found time to finish up Kmers.jl. My plan is to release Kmers.jl 1.0 in a couple of months.

---

<div class="post-metadata">

**Author:** ![kevbonham](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/kevbonham/32/216165_2.png) [@kevbonham](https://discourse.julialang.org/u/kevbonham)\
**Post date:** [December 31, 2023, 12:10pm UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203/2 "2023-12-31T12:10:50Z")

</div>

Huge thanks for this effort, and for the detailed history and explanation! I will happily give it a test drive!

Happy New Year 🎇

---

<div class="post-metadata">

**Author:** ![camilogarciabotero](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/camilogarciabotero/32/35000_2.png) [@camilogarciabotero](https://discourse.julialang.org/u/camilogarciabotero)\
**Post date:** [December 31, 2023, 5:12pm UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203/3 "2023-12-31T17:12:07Z")

</div>

Thank you @jakobnissen and all that put effort into this project. I think this package is a cornerstone of other bioinfo packages. I will take a look and be happy to give some feedback. Best.

---

<div class="post-metadata">

**Author:** ![jakobnissen](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/jakobnissen/32/13477_2.png) [@jakobnissen](https://discourse.julialang.org/u/jakobnissen)\
**Post date:** [December 23, 2024, 4:31pm UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203/4 "2024-12-23T16:31:51Z")

</div>

Thanks for the feedback, all! Kmers v1.0.0 is now released and available to download.

---

<div class="post-metadata">

**Author:** ![evanfields](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/evanfields/32/1744_2.png) [@evanfields](https://discourse.julialang.org/u/evanfields)\
**Post date:** [December 23, 2024, 6:38pm UTC](https://discourse.julialang.org/t/request-for-comments-upcoming-kmers-jl-version-1-0/108203/5 "2024-12-23T18:38:07Z")

</div>

Congrats on and thanks for the release! I use the BioJulia ecosystem every [work]day (and might do a high performance kmer counting project in Q1), so I’m excited to see what the new Kmers API is like.