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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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From https://sourmash.readthedocs.io/en/latest/using-sourmash-a-guide.html#how-do-i-store-and-search-collections-of-signatures I expected to be able to pass a folder name to mean all the signatures in…
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https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/504 fixes a bunch of issues where `scaled` was not being set properly, ref https://github.com/sourmash-bio/sourmash/issues/3384. This l…
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As of sourmash_branchwater_plugin v0.9.9, this error message will be returned in certain circumstances - the easiest way to trigger it is to use a pathlist that points at a `.sig`/`.sig.gz` file that …
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once https://github.com/sourmash-bio/sourmash/pull/3342 is merged, along with https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/471, I think we have a nice chance to consolidate down to…
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hi nice people,
I'm interested in doing some sourmash-y stuff with ATB, for which we would need to sketch the genomes. @iqbal-lab mentioned that this was in process [over on bluesky](https://bsky.a…
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one of the upshots from the benchmarks in https://github.com/sourmash-bio/sourmash_plugin_branchwater/issues/479 is that fmg x rocksdb doesn't use multiple cores and is also I/O bound. This is presuma…
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https://github.com/sourmash-bio/sourmash_plugin_branchwater?tab=readme-ov-file
sourmash plugin pour utilisation en multithread. En gros, en ce moment la fonction Sourmash gather n'est pas paralléli…
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code in #40 could benefit from making `SeqToHashes` less opaque over in sourmash.
Some ideas:
* simple and lightweight: provide access to `kmer_index` per https://github.com/oxli-bio/oxli/pull/4…
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### Description of feature
Example workflow: https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/