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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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Following the same process as sourmash-bio/sourmash#2410, we will benchmark the genome-grist workflow with a combination of the six sequences listed in the sourmash-bio/sourmash#2410. My instinct is t…
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when I run:
```
sourmash scripts multisearch zip-without-manifest.zip zip-with-manifest.zip -o zzz.csv
```
I get:
```
=> sourmash_plugin_branchwater 0.9.3.dev0; cite Irber et al., doi: 10.1101…
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Is this intentional?
https://github.com/sourmash-bio/sourmash_plugin_branchwater/blob/43caeba6833a7efbdacc98b3cfbf56ae8867110e/src/utils.rs#L651-L659
https://github.com/sourmash-bio/sourmash_plug…
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Transferred issue from genome-to-json, original openend by AgressiveHayBale:
The "Warning, less than 50 percent could be taxonomically assigned to analysed genome" message is unclear when Sourmash pr…
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sourmash commands allow search / gather across multiple databases. We could enable that here too.
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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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So, I did a thing, and I don't really know how to evaluate it. Thoughts welcome!
## summary: DNA and protein
so I gristed a bunch of the Northen data sets, using both DNA searching (against all …
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When we run:
```
scripts manysearch zip-with-manifest.zip zip-with-manifest.zip -o foo.csv
```
it works fine; but with
```
sourmash scripts manysearch zip-without-manifest.zip zip-without-manife…
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since I'm rebuilding some of the SBTs and I've been doing a lot of indexing, I'm finding the overly verbose output of index and lca index to be annoying. I get pages and pages of :
```
Error in pa…