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per #1598,
@ctb says:
> in `ZipFileLinearIndex`, we have to break `Storage` encapsulation and go directly to the zipfile to get a list of all files, in cases where there is no manifest. (Listing a…
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* NCBI taxdump format
* greengenes tsv format
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see https://github.com/dib-lab/charcoal/commit/4838253a5677e3c64e50cd621308772116bbea81 for example code
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I plan to implement the kSpider's algorithm in Rust, utilizing the inverted index of RocksDB. I wanted to ask if that should be another sub-command in the `branchwater pairwise` or if it should be a s…
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Hi dear developers. I am thoroughly enjoying sourmash currently within my little project. However, I see that sourmash is running maximal 100% of CPU. I wonder, it is possible to add multithread and e…
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revisiting a (5 yro :) conversation about interoperability https://github.com/marbl/Mash/issues/27 after some discussions on slack with @kescobo on [µbioinfo slack](https://microbial-bioinfo.slack.com…
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Construct databases using the same refseq data as the `kraken2` database which includes
- complete genome, chromosome, scaffold and contigs
- Archaea, Bacteria, viral, protozoa, fungi, plasmid…
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Dear sourmash team:
Good afternoon.
After the initial analysis, I get the specific K-mers list in fasta form.
For further analysis, how to extract the paried reads from the original fastq fil…
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Some ideas rescued from https://github.com/dib-lab/sourmash/issues/1142 -
* `load_file_as_signatures` doesn't take a string input, per https://github.com/dib-lab/sourmash/pull/1304. This challenges…
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when I run
```
twine upload sourmash-4.8.0-py3-none-emscripten_3_1_32_wasm32.whl
```
I get:
```
Uploading distributions to https://upload.pypi.org/legacy/
Uploading sourmash-4.8.0-py3-none-emsc…