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$P$(observe k events) =
Here the parameter $\lambda = \frac{M}{S}$ is the expected number of hashes
for $M$ k-mers at a scaled of $S$.
$P$(k hashes for M k-mers with scaled S) = ${\exp(-M /…
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Hello ! Thank for the work you've done, it i going to save a lot of time !
I recently read '_k_-nonical space: sketching with reverse complement' [Oxford bioinformatics](https://academic.oup.com/b…
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as plugins proliferate (good? bad? who knows!) there seems to be a need for providing better docs and functions for plugins to make use of sourmash library code.
areas where I see this need most cl…
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(this can be a bit of a running issue until we get around to fixing them ;)
The introduction of ANI output in [v4.4.0](https://github.com/sourmash-bio/sourmash/releases/tag/v4.4.0) is pretty awesom…
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As I was thinking about the ANI stuff #1967 https://github.com/sourmash-bio/sourmash/issues/2001 I came up with an idea. 💡
right now, search outputs largely useless CSV files, with minimal informat…
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with sourmash v4.4, sourmash can now estimate Average Nucleotide Identity between genomes: this is the fraction of bases that would be identical in a pairwise alignment. However, sourmash estimates th…
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Hi,
Could you help me to understand how QueryContainmentAni and MatchContainmentAni are calculated?
Given the use of exact kmer matches, I would assume that the ANI between a query kmer and a re…
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when we see a number like "50%" in containment it could be caused by missing content (e.g. low coverage but otherwise exact matches) or strain variation. It seems like we should be able to do a k-mer …
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Hello, database docs said:
> The signatures were calculated with a scaled of 1000, which robustly supports searches for ~10kb or larger matches.
>
I want to know how "~10kb" were estimated, and d…
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Ref #606.
The reviewers for [Pierce et al., 2019](https://f1000research.com/articles/8-1006) were enthusiastic about some of the algorithmic ideas we hinted at in sourmash (and correctly pointed ou…