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black for Python
maybe [rustfmt](https://github.com/rust-lang/rustfmt) for rust?
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we could allow `sourmash sketch` to take `name=` in param strings, e.g.
`sourmash sketch dna -p k=31,name='cool name, luke'`
rationale: when writing up the docs for sourmash sketch per https://g…
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Hello,
I've been using protein k-mers from sourmash to compare single-cell RNA-seq profiles across different species. I'm curious to benchmark `dashing` for this purpose as well.
Warmest,
Olga
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per @mr-eyes -
>I was trying yesterday to generate lineage information and follow the format as in all_genbank_lineages.20200727.csv and I started using taxonkit reformat for that purpose but still…
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In #1493, we added `sourmash_args.SaveSignaturesToLocation(...)` to support a wide variety of output formats.
In #1891, we are adding the ability to read manifest files, as output by `sourmash sig …
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review comment: https://github.com/sourmash-bio/sourmash_plugin_branchwater/pull/234#issuecomment-1966691225
> could you add some minimal benchmarks (time/memory) for a standard-ish comparison, e.g…
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deal with this warning from the docs in #21 -
>**Warning:** At the moment, if two different queries have the same `{basename}`, the CSVs for one will be overwritten. The behavior here is undefined …
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Hello there!
I'm interested in using `khmer` to count and filter kmers from transcriptome datasets and then use the raw kmer counts across multiple (~10) samples as the "X" matrix for a classificatio…
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Hi @ctb,
I built a test database where I duplicated a genome but given two different names `48246288` and `482462`:
```
internal_location,md5,md5short,ksize,moltype,num,scaled,n_hashes,with_abun…
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In cluster, we build the graph from scratch each time. Would be great to allow input of another set of clusters or an existing graph that could be updated.