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calc-hash-presence.py from [pangenome-hash-cor](https://github.com/ctb/2024-pangenome-hash-corr), does not yet allow me to compare protein sketches instead of nucleotide sketches.
I'd like to comp…
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I am using the add_hash_with_abundance method to add pre-calculated kmers with their abundances. Can this work with a scaled minHash? Will the order or kmers streaming in matter?
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Ref #606.
The reviewers for [Pierce et al., 2019](https://f1000research.com/articles/8-1006) were enthusiastic about some of the algorithmic ideas we hinted at in sourmash (and correctly pointed ou…
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Dear Camille,
Many thanks for making the "Sketching in sequence bioinformatics: methods and applications" slides open source. Several questions related to bottom-s MinHash, One Permutation MinHash …
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(issue triggered by https://github.com/dib-lab/sourmash/blob/66461a4665471a5c0a2c5df02f8180c7ecaf5726/tests/test_signature.py#L51-L52)
Some API thinking: should we make `n=0` the default, and allow…
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At the moment, we use `signature::select` to downsample minhashes if needed. However, this means we load the minhash during the `select`, which may happen during `sig_for_dataset`, for example, and th…
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I have questions.
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https://hackmd.io/RScxLBU-SCiEjdNHrJql5w
# FracMinHash vs MinHash pseudocode
## FracMinHash
Here the `scaled` parameter is tunable, and `H` is the size of the hash space (e.g. 2**64).
Note…
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Since `sourmash sig describe` was added (https://github.com/dib-lab/sourmash/pull/587), one can now output a CSV summarizing the k-mer sizes, molecule types, number of hashes, etc from each MinHash sk…
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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…