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Once https://github.com/sourmash-bio/sourmash/pull/1967 is merged, ANI will available in CSV files! 🎉
It is also available in `sourmash compare` matrix output, if `--ani` is used. 🎉
I don't _t…
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This is more of an FYI than a bug.
The accession numbers shown in the database tutorial at
https://sourmash.readthedocs.io/en/latest/tutorial-basic.html#make-and-search-a-database-quickly
are mis…
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I have a suggestion that may be considered for a future version of sourmash. The current Minhash includes `hashes` and `abundances`. I propose adding an optional array called `positions`, which would …
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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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here are some thoughts I wrote up for a collaborator, thought I'd share broadly -
The default FracMinHash approach will yield overlap estimates when applied to two metagenomes. In technical terms t…
ctb updated
10 months ago
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Dear sourmash team,
I've recently attempted to create a minimal test dataset and encountered an error when using `sourmash gather`.
Specifically, it raises an `AssertionError`.
I think that t…
vmikk updated
8 months ago
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(copied from https://github.com/sourmash-bio/sourmash/issues/461#issuecomment-1993390314)
Hi Titus @ctb , I don't know whether I could ask the following questions related to this issue, anyway....
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Hi Jim,
I need to compare FracMinHash with Minimizer + MinHash to see their Jaccard estimation accuracy. The key step in both is the sketch size for MinHash and FracMinHash: FracMinHash is in the o…
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Hello Hyper-Gen team,
New version of Minhash-like algorithm called one permutaiton minhash with optimal/faster densification is by far the fastest and theoretical limit of such algorithms, implemen…