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yesterday, I spent some time digging into a sourmash use case with @shannonekj, and a few different reasonably generic utility script needs emerged.
the code for this is [in a private repository](h…
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lots more people are doing comparisons between sourmash output and other tree/dendrogram/clustering approaches. it would be nice to better support that with nicer output formats.
we could also anno…
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despite https://github.com/dib-lab/sourmash/issues/1571, the problems in #1552 continued after using the new `remove_many` implementation until I refactored the enclosing script in #1613.
The follo…
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With the updated rust core, we need to go through and rationalize (and unify) rust and python code so we don't, for example, create sigs/zips that break rust assumptions.
from luiz: rust and python…
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we should point people at GTDB papers, and other.
also, taylor's olive genome preprint.
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This is an update of & replacement for https://github.com/dib-lab/sourmash/issues/1072, which introduced the idea of a `database.select(...)` function.
This issue is being updated after the release…
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This is an update of and replacement for https://github.com/dib-lab/sourmash/issues/999, which raised a lot of issues around how we were doing protein k-mer calculations.
This issue is being update…
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Currently, I manually transferred the matched genomes from the gather output to the snakefile; this workflow will still run in a fully automate fashion, but selecting which genomes to download and dow…
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in particular maybe add tSNE... others?
https://hdbscan.readthedocs.io/en/latest/comparing_clustering_algorithms.html
https://naomy-gomes.medium.com/k-means-clustering-explained-with-python-c7c6…
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I might be wrong here, but it looks like the scipy linkage call invoked for the dendrogram is silently producing misleading output. The function signature for linkage expects either a condensed format…