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ref ANI estimation PR #1788
I've been using our forthcoming ANI utilities to estimate pairwise ANI between GTDB genomes. From these data, we can examine the average containment --> ANI relationshi…
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In re this paper,
[Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances](https://www.biorxiv.org/content/10.1101/2022.01.11.47587…
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@drtamermansour asked some questions on slack about how FracMinHash signatures with different scaled values are handled in practice, and I took a look in the docs and couldn't find anything that was c…
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We want to include `sourmash` as an alternative for calculating ANI values. This will be a new feature, currently not available in the existing `pyANI`, so we need to investigate the best approach in …
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curious how well our underlying infrastructure can work for handling other kinds of fracminhash sequences! maybe could be explored using plugins.
https://github.com/St4NNi/jam-rs
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per https://github.com/sourmash-bio/sourmash/issues/267#issuecomment-1117633898
@dkoslicki says:
> In the FracMinHash sketches, does sourmash save the k-mers that led to the hash values, or just t…
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https://hackmd.io/RScxLBU-SCiEjdNHrJql5w
# FracMinHash vs MinHash pseudocode
## FracMinHash
Here the `scaled` parameter is tunable, and `H` is the size of the hash space (e.g. 2**64).
Note…
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revisiting a (5 yro :) conversation about interoperability https://github.com/marbl/Mash/issues/27 after some discussions on slack with @kescobo on [µbioinfo slack](https://microbial-bioinfo.slack.com…
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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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Per: https://github.com/ctb/2022-sourmash-sens-spec/blob/main/fracminhash-runs-simulate.ipynb
```
in M=100 k-mers, p of finding at least one hash is: 63.43% - scaled=100
in M=200 k-mers, p of fin…