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Over in https://github.com/dib-lab/genome-grist/pull/107#issuecomment-1019274050, @mr-eyes asked -
> > Wanted to ask, was there a specific criterion for selecting the abundtrim and trimming paramet…
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@drtamermansour asked some questions on slack about how FracMinHash signatures with different scaled values are handled in practice, and I took a look in the docs and couldn't find anything that was c…
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### Description of the bug
See here: https://nfcore.slack.com/archives/C062H82UCRG/p1710513463929289?thread_ts=1709737644.063319&cid=C062H82UCRG
I think we can just supply the entire work director…
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over in https://github.com/sourmash-bio/sourmash/pull/2256, I have an experimental PR that adds direct loading of .sig files (JSON format) via HTTP GET, using the `requests` library. It's remarkably s…
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I think it would be helpful to include in the sourmash documentation on how to interpret the charts and graphs that sourmash produces.
I may suggest
- adding information in a [side text](https://…
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```
find -maxdepth 1 -type d -name '[!.]*' -exec du -sh {} + | sort -h > dir_sizes.txt
```
produces output
```
392M ./spacegraphcats
595M ./bcalm
733M ./stamps_tut
908M ./2021-…
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Hi!
It would be practical to allow the ````sourmash compare```` command to output for example both Jaccard similarity and Containment similarity in one run.
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**1. A function that reads a sourmash signature file/database and raises exceptions if it runs into issues**
```
db = load_file_as_index(filename)
```
returns `None` if the file cannot be loa…
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PR https://github.com/dib-lab/sourmash/pull/882 raised a question in my mind about the various similarity and comparison methods on MinHash objects. We have `similarity`, `compare`, and `jaccard`, as …
ctb updated
10 months ago
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MurmurHash, while relatively fast / dispersive / backwards compatible with Mash, is slower than some newer algorithms. Moving to xxHash should yield a ~2X speed improvement in the hashing portions of …