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It was pretty clear early on in testing the banding functionality that it would not play nicely with the 2-bit hashing scheme in khmer. My first approach to banding was to look at bit patterns (`for b…
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Currently, several functions exposed in python-land are case sensitive in regards to hashing. For example,
1. get
2. forward_hash
3. consume -- not sure
The result is that python code which deals dir…
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I have a simple/naive thought re reverse-hashing the kmers. We can provide an option to Minhash `reversible = True` to use a reversible hashing function like the Integer Hashing to retrieve back canon…
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As seen in #701, the way the MinHash object interface works for protein MinHashes is undocumented and quite possibly just stooopid.
A few issues:
* per [this comment](https://github.com/dib-lab/…
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In recent runs against the latest NCBI dataset of Listeria, we've observed large discrepancies between RabbitTClust and NCBI clustering results. Here're a few examples.
1. When distance threshold < …
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[Idea here](https://twitter.com/lh3lh3/status/1037487551504896001).
Murmurhash is fast, but it would potentially be faster to use a hashing function (like [ntHash](https://github.com/bcgsc/ntHash) …
bovee updated
5 years ago
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spacegraphcats.cdbg.index_cdbg_by_kmer is both slow and memory intensive, sigh.
speed may require more Cythonization or something.
in terms of memory intensitivity, one problem right now is that…
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Hi
We are working on analysis of Bioinformatics tools (related to Kmer counting) and Gerbil is one of them. We have gone through **readme** file and it is very helpful. As we are doing analysis so…
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Dear Kraken2 developers,
I'm using your excellent kraken2 software in my metagenomics project and have read through your paper on kraken2. And I am really confused about its database buildi…
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This is a feature request (as discussed with @bluegenes earlier today) to have the k-mers that correspond to the hash values also returned when doing a `sourmash sketch`. I was made aware of [sourmash…