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I am trying to run a `foldseek easy-search` job with the UniProt database built from `foldseek databases Alphafold/UniProt`. With two different attempts on different machines (with up to 256GB memory)…
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[extract-max-extent-around-hashes.py](https://github.com/ctb/2022-sourmash-sens-spec/blob/main/scripts/extract-max-extent-around-hashes.py) is a potentially useful script that does the following:
G…
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Are k-mers with ambiguous nucleotides (e.g. N) included in the sketch or are they thrown out?
I would imagine the best strategy is to have Mash filter these kmers out. I suppose it could be handle…
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I was wondering if it would be possible to add a function to BitFieldVec that would allow extract multiple elements and returning them in the underlying word type. My specific use-case is this (but I…
rob-p updated
1 month ago
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I created a pangenome graph using pggb, resulting in gfa and og files. I now wish to perform some mappings to the graph and have a few questions:
1. From the pggb documentation I understand that the …
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I have an RNA seq that I need to assemble from PacBio and when I send the script the program do not pass the stage 2. I work with PACbio long read Hifi sequence that end up being all around 12 mil…
A-pcd updated
1 month ago
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Hello,
and thank you for this amazing tool. I am currently examining different methods of hybrid de novo transcriptome assembly.
I constructed various assemblies from mouse data and compared their…
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Hello,
Thank you for developing kmc.
I ran into an issue today before I realized I was using the wrong flag.
When using -fa instead of -fm, kmc (v3.2.1) runs smoothly but obviously produces inc…
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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