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while working on https://github.com/sourmash-bio/sourmash/pull/2225 and making sure that `plot` will work with both similarity and distance matrices, I ran a few comparisons with the 64 genomes from p…
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Hi,
I have pairs of metagenomes that I want to compare the similarity of them as well as figure out the % of one metagenome that is contained within the other one. sourmash gather & search seem to …
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The CLI plugin system introduced in https://github.com/sourmash-bio/sourmash/pull/2438 is (to my mind ;) pretty nice - maybe we could refactor the sourmash CLI code to look like this more generally?
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Hi SourMash authors,
We recently used your tool to annotate our reads, assembled contigs, and assembled genomes, and found that if we pool all contigs into one fasta, we cannot see the annotate res…
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So, this occurred to me yesterday: What if we make the Python API look like the CLI?
Let's say I want to call `sourmash sig describe ` in Python. I'm not even sure how to do it now, but it would be…
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So I did a thing... https://github.com/ctb/2021-sourmash-greymake
Building off some conversations with @bluegenes, and inspired a bit by the work on manifests of manifests https://github.com/sourma…
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Trying again to run the Demo from the instructions, but this time, there is something broken with respect to LineagePair from sourmash.lca.
I also don't know why in the output it says == This is so…
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[env-reporting.yml](https://github.com/dib-lab/charcoal/blob/latest/charcoal/conf/env-reporting.yml) is the largest and most complex conda environment we have in charcoal, and it pins a lot of things.…
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As noted by Titus in [an issue](https://github.com/marbl/Mash/issues/27), Minhash sketches should be stable and cross-compatible between programs. It makes sense to fall into line with this convention…
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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…