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I'm interested in finding the location of kmer which are present twice in a genome fasta file.
I collect these kmers using kmc and transform the kmc dump to fasta before running klocate.
When I …
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[Tue Nov 5 13:52:15 2024] Read in and count kmers for 112200000 reads.
[Tue Nov 5 15:05:27 2024] Found 109640387 reads.
[Tue Nov 5 15:07:42 2024] Finish sorting the reads.
[Tue Nov 5 15:15:52…
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张老师好！ 我组装了一个2倍体基因组, 因为做kmer分析的时候, 整个基因组的杂合度很高, 所以选择装出两套单倍型基因组，我想用subphaser来对这两套单倍型基因组进行分型, -f 参数默认是2，如果我使用-f 默认参数就显示ValueError: 0 kmer remained after filtering. Please reset the filter options. 后来我将-f…
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How fast can we make kmer counting in Rust?
@ctb, are there examples of this from Sourmash or other libraries?
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Hi Ren:
I am a phd student from SYSU, China. I have asked you some questions before and you are so patient to answer my questions. Now I have encountered one problem when using the tool "VirHostMa…
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Hi all, thanks for this MMseqs2 that seems very efficient.
Unfortunately it seems to not be willing to run on my machine :
mmseqs easy-cluster /Users/s/Documents/Albatros/protein//short_name-Gr…
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A miscellaneous collection of thoughts that are not big enough or well enough formed to put in their own issues, but should be noted somewhere.
We may be double-hashing things - hashing the hash va…
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Where does the unique.skf file go once we run "ska unique"? Are there any limitations to this that we should know of?
My command runs and does not give me an error. I get the following:
`Output wil…
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Hello,
I am currently facing an issue with extremely high memory usage while building a Kraken2 database with around 400GB of genomes. When using a 31-mer size, the database construction seems to r…
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Would it be okay to switch:
https://github.com/KwanLab/Autometa/blob/0d9028cf7bad20d6e28667aaba9d3889a15ace09/autometa/common/kmers.py#L601-L607
to adapt to a lower pca dimension when there aren…