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Also need to add this feature to multiqc ... but would be helpful to get a summary of number of kmers and such per signature
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Hello,
I am keen on trying this tool on our data! I already have kmers calculated by Jellyfish. However, I am not sure how to proceed further. Can you please provide at least a sample sequence of com…
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Hi,
I want to plot kmer values of direct RNA sequenced samples, and got it to work successfully, but it appears that C and U center bases have the lowest signal, while A and G center nucleotides h…
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This is perhaps an interesting datum. Building the PRG (by which i mean "gramtools build") for 1.3kb of the TB genome, combining calls from 50,000 TB, we find there the max alphabet number is 420 - s…
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Hi, thanks for this useful software,
I was using this tool, and currently wondering if it is possible to generate a affinity table for each enriched k-mer in a library. I found one tool in bioconduc…
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this might be of use to people looking to grok genome overlaps etc.
[notebook permalink](https://github.com/dib-lab/genome-grist/blob/051a96210958afcf7f1d61ce11537796339dc64e/hash-upsetr-example.ip…
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I wanted to use `Maast`'s sck-mer database construction command `db` on a set of VCF, MSA Fasta, and reference.fna (Klebsiella _pneumoniae subsp. pneumoniae_ reference genome KPNIH1) files which are …
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For example -
```
cat test_hist1.txt | head
abundance,count,cumulative,cumulative_fraction
2,1,1,0.0
4,2,3,0.001
5,2,5,0.002
6,3,8,0.004
9,1,9,0.004
10,4,13,0.006
11,1,14,0.007
12,2,16,0.…
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BitTree: https://github.com/lynxoid/bit_tree_cpp
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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…