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Hi there,
I am actually running kmer-db as a part of SqueezeMeta's dependencies, but even when I do a fresh install via conda in a new environment (versions 1.11.1, 1.7.6, or 1.9.2), and run kmer-d…
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The insert function has to check its input. If integer, it should be
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Would an option to ignore over-occurring kmers make mash more robust against large repeat families and multi-copy plasmids?
mash estimates the coverage in -r mode, and it uses -m for a min freq, bu…
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Thanks for the great software package, it's been great to use.
It is my understanding that the BFT shouldn't return false-positive kmer hits, is this correct?
If I'm correct, I think I've come a…
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Is there potential to add larger kmer values as user input? Might require refactoring of the code which writes to output.
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## Expected Behavior
mmseqs easy-cluster should finish without errors.
## Current Behavior
```
Query database size: 19552 type: Nucleotide
Estimated memory consumption: 8G
Target database …
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## Description
Replace the uses of `Eigen::SparseMatrix` (e.g., in CSR multiply) with more efficient custom code. As an example, @blackwer wrote faster code than Eigen for a project we did here on…
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## Expected Behavior
[dataset.zip](https://github.com/user-attachments/files/16023829/dataset.zip)
I have a group of sequences which is properly aligned with almost full length and >95% identity usi…
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Requested feature: enable defining a custom kmer alphabet
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The `_shred` method returns a ordered list of kmer IDs. Assert two subsequent kmers in the list are neighborly (share a k-1 mer in common) or else do not increment that edge (it mustn't exist)