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Also need to add this feature to multiqc ... but would be helpful to get a summary of number of kmers and such per signature
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@ctb I remember reading your blog about one use for sourmash and YAML would be to connect different researchers together.
I was wondering if such a database could help both to connect researchers and…
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I thought this might be of interest to folks using sourmash. I am sitting on 80+ metagenomes from bats. We swabbed their external surfaces (i.e., furred surfaces, ears, wings and uropatagia). I ran so…
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This is an expected limitation in sourmash when working with signatures in Python data structures. Python dictionaries are restricted in the amount of data they can hold, regardless of available RAM.
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over in In https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/213, I tried to describe standalone manifests and their benefits for lazy loading. I wrote:
>
> There are various pla…
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a better? or at least more understandable? version of https://github.com/dib-lab/sourmash/issues/333
see gist at https://gist.github.com/ctb/85fe2efb23b70bbd72ea6a69750d1284
# the README from th…
ctb updated
11 months ago
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Had a question on whether `manysearch` results are ordered by best hit, and whether we could add a threshold parameter to return only the top n results.
I think:
- non-rocksdb `manysearch` are ord…
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ok, I've got the containment figure (figure 1) working with sourmash now.
The notebook is `containment/notebooks/containment-plot.ipynb` in the https://github.com/dib-lab/2021-paper-sourmash-gather…
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should be intersect_bp, I think? to match sourmash => multiply by scaled.
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can we use it to store SBTs and minhashes? (c.f. https://github.com/dib-lab/sourmash/)
can it be used as a Jupyter Notebook file system?
what about a purely JavaScript upload/download app?