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Hi! Thanks for the great tool! I was wondering if one could get the genomic location of subgenome-specific TE or TE k-mer. My idea is to take a look at coding regions that are upstream and downstream …
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I've been trying to get metalign up and running for a metagenomics project I'm working on. I originally realized when I cloned the github repository, the db_info.txt file was not present and was givin…
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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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Hi,
Is it possible to extract the k-mer and/or minimizer sequences assigned to a specific taxon from a Kraken2 database file?
Thanks,
-Bob
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In Part 2, for Question 5, my Barplot for E.Coli Under-represented K-mers seems to be missing some of the K-mer names on my x-axis.
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I was seeking a similar kind of "one number measure" to unicity distance, but for _taxonomic_ incoherency, and I decided to try out k-mer Shannon entropy - [link](https://en.wikipedia.org/wiki/Entropy…
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## Expected Behavior
Summary: Running linclust or clust with a very big database leads to a heavy slowdown in the rescorediagonal part. Expected the job to continue much faster. It releases a warning…
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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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Hello! I am working on replicating some (amazing) work from Taylor's [IBD project](https://www.biorxiv.org/content/10.1101/2022.06.30.498290v1.full).
I have signatures from `sourmash sketch dna` of…
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Hi,
I have met with another ignoring error, here is the log:
0.982908 k-mers per position
14994 DB matches per sequence
8 overflows
0 queries produce too many hits (truncated result)
58 sequen…