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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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Currently, yass runs with only single threads, and is slow for large fasta files.
Is it possible to speed up yass by running parallelly on more threads?
Thanks.
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Enhancement:
I am thinking we could have a ntHash iterator with a phred filter. basically we could add a member which is a rolling sum of the Phred quality rather than the average. Every time we comp…
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#### Describe the bug
While working on https://github.com/conda-forge/scikit-learn-feedstock/pull/123, I found that `manifold/tests/test_t_sne.py::test_uniform_grid[barnes_hut]` fails on ppc64l…
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Hello,
I don't know if you are accepting suggestions for improvements, but I was wondering if you were perhaps open to implementing [geometric hashing](https://www.biorxiv.org/content/10.1101/2020.…
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```
________________________ test_uniform_grid[barnes_hut] _________________________
method = 'barnes_hut'
@pytest.mark.parametrize('method', ['barnes_hut', 'exact'])
def test_uniform_…
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I am trying to determine, whether to add sequence searching by diamond to our website https://biocyc.org/ , in addition to blast based searches. BioCyc nowadays has about 18000 genomes (mostly bacter…
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A user has reported that they see a `Not a valid bip39 mnemonic` error message when entering their 24-word Trezor recovery phrase in software mode with v4.0.4 that was previously used with the v3.x wa…
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I see this in the build log being raised from the FN2 checkit:
```
File "/usr/lib/python3/dist-packages/sage/plot/graphics.py", line 2404, in _matplotlib_tick_formatter
raise ValueError('Expa…
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## Background
The "Random-number generation" section of `vignettes(topic = "parallel", package = "parallel")` describes concerns about pseudo-random numbers in parallel computing. If we have differ…