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provide/update/refactor documentation around k-mer sizes and scaled #2918

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ctb opened this issue Jan 13, 2024 · 1 comment · Fixed by #2921
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provide/update/refactor documentation around k-mer sizes and scaled #2918

ctb opened this issue Jan 13, 2024 · 1 comment · Fixed by #2921

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@ctb
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ctb commented Jan 13, 2024 •
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per @LilyAnderssonLee review

I may have overlooked it in your documentation. It would be helpful if you could provide some recommendations for the selection of k-mers and scales.

and

What are the consequences of using different scales? Do you recommend using the same scale to generate the signatures for genomes or databases?
@ctb ctb mentioned this issue Jan 13, 2024
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ctb commented Jan 14, 2024

Partially answered here https://sourmash.readthedocs.io/en/latest/using-sourmash-a-guide.html#what-k-mer-size-s-should-i-use and here https://sourmash.readthedocs.io/en/latest/using-sourmash-a-guide.html#what-resolution-should-my-signatures-be-how-should-i-create-them. I think we should add a pointer to this in the FAQ to make it more discoverable, and also highlight this section:

One additional wrinkle is that we provide a number of precalculated databases at k=21, k=31, and k=51. It is often convenient to calculate signatures at these sizes so that you can use these databases.

@ctb ctb mentioned this issue Jan 15, 2024
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@ctb ctb closed this as completed in #2921 Jan 15, 2024
ctb added a commit that referenced this issue Jan 15, 2024
@ctb @ccbaumler
MRG: add scaled FAQ, adjust ksize answer (#2921)
11af4d5 
Adds the following FAQ entry to address
#2918:

> ## What scaled values should I use with sourmash?
> 
> We recommend scaled=1000 or scaled=10000 when working with bacterial
> and archaeal sketches and DNA. We have quite a bit of experience with
> this, and even some
> [published
benchmarks](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-05103-0)
> showing that this works very well.  You may need to use lower scaled
> values with smaller query and target sequences, such as viral genomes
> or genes, but we do not have systematic advice on this.
> 
> That having been said, you can always use a lower scaled value - the
only
> consequence is that memory and compute requirements increase.
> 
> Also, sourmash will automatically use the larger of two scaled values
> when comparing two sketches with different scaled values. So if, for
example,
> you use [the precomputed databases](databases.md), you will always end
up
> using your query sketches at a minimum scaled of 1000, even if you
created
> them with a lower scaled value.
> 
> Please also see [What resolution should my signatures
be?](using-sourmash-a-guide.md#what-resolution-should-my-signatures-be-how-should-i-create-them).

Fixes #2918

---------

Co-authored-by: Colton Baumler <63077899+ccbaumler@users.noreply.github.com>
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MRG: add scaled FAQ, adjust ksize answer sourmash-bio/sourmash
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