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When working with [the SRA](https://www.ncbi.nlm.nih.gov/sra/), a list of accession numbers may be exported. To insert that list directly into a `config.yml` file for use in genome-grist, we can use t…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…
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there's a conflicting PyPI package named [charcoal](https://pypi.org/project/charcoal/) and so I named this charcoal `charcoal-bio` in the setup.py.
However, the package is still `charcoal`, the CL…
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Hi Titus et al,
Given the recent fiasco related to mapping reads to microbial databases without human references (links at bottom), it might be a good time to create a small human genome database fo…
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e.g. if a chromosome from a genome sequence has a single non-ACGTN in it, the entire sequence will be ignored. This is unexpected.
This should probably be changed so that such k-mers can be skipped…
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Hello,
If I wanted to do exact k-mer comparisons between genome assemblies could I simple use `sourmash sketch` with `scaled=1`?
Is this a stupid thing to do?
I have a limited set of bacterial…
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I calculated signatures like this:
```
sourmash compute -o {output} --merge {wildcards.sample}_mgx --scaled 2000 -k 21,31,51 --track-abundance {input.r1} {input.r2}
```
and used `sourmash sig…
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This would be used in cases where non-complex metagenomes do not require a high amount of sequencing coverage to capture all of the necessary information.
It would be an option for dahak users to i…
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prefetch and gather use different CSV column headers for their output, and I'm sure so does search and other commands.
Would be good to fix this in v5.
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Over in https://github.com/dib-lab/sourmash/issues/1511#issuecomment-855262248, I've been building new LCA databases for GTDB rs202, and (after resolving the duplicates problem in #1568 :) I was still…