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This is not really an issue, just a suggestion -- hope all is well!
We are finding new ways to use SEEKR by specifying custom alphabets. In these experiments, we are encountering words or k-mers th…
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Hello,
I've been using protein k-mers from sourmash to compare single-cell RNA-seq profiles across different species. I'm curious to benchmark `dashing` for this purpose as well.
Warmest,
Olga
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Hello
I would like to count equally spaced k-mers.
e.g.) in-frame k-mers (such as codons or bi-codons) with step size 3.
Is it possible with Jellyfish?
Thank you
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Hi,
when I try to run vargeno on the same data linked in my previous issue (https://github.com/medvedevgroup/vargeno/issues/2), it crashes during the geno step.
This is the output of `vargeno inde…
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Would it be possible in `compare` or `index` to include a TF-IDF-style step that reweighted the k-mers based on their "rareness" in the corpus? i.e. k-mers that are ubiquitous would receive a lower we…
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I have a weird issue with ploidyplot. It was working fine before:
```
PloidyPlot -e12 -k -v -T38 -o/smudgeplot/kmerpairs /smudgeplot/FastK_Table
Activating conda environment: .snakemake…
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Hi,
I have a question about the output from
`./dashing cmp –k10 -p5 -C -S24 --wj-exact reference_.fasta reads.fastq`
The output i.e. 0.0005 (says that 0.05% of the k-mers in the union are shared)…
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I am trying to build an index for NT (NCBI non-redundant nucleotide database). I am using a machine with 96CPUs and 756GB, I have tried:
`metagraph build -v -k 31 -o graph -p 96 --disk-swap /mnt/tmp…
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### Description of bug
I am running metaSPADES on a co-assembly of 6 samples totalling 19gb raw reads given to metaSPADES. Despite this being a somewhat typical size of metagenomic dataset I get out …
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I built a Kraken1 database and I'm trying to generate the corresponding bracken distribution file.
Everything went well until I got a segmentation fault at STEP 4 (CONVERTING KMER MAPPINGS INTO REA…