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MRG: update with misc animal genomes #3422

Merged
merged 2 commits into from
Dec 8, 2024
Merged

MRG: update with misc animal genomes #3422

merged 2 commits into from
Dec 8, 2024

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ctb
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@ctb ctb commented Dec 7, 2024

Adds common hosts and also hg38.

Tackles #2717

Screenshot 2024-12-07 at 9 17 40 AM

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codecov bot commented Dec 7, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.43%. Comparing base (0f48dc5) to head (dc9d435).
Report is 1 commits behind head on latest.

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@@            Coverage Diff             @@
##           latest    #3422      +/-   ##
==========================================
- Coverage   86.44%   86.43%   -0.02%     
==========================================
  Files         137      137              
  Lines       16103    16103              
  Branches     2219     2219              
==========================================
- Hits        13920    13918       -2     
- Misses       1876     1878       +2     
  Partials      307      307              
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python 92.40% <ø> (ø)
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ctb commented Dec 7, 2024

Ready for review & merge @bluegenes @ccbaumler !

doc/databases.md Outdated
@@ -30,6 +30,20 @@ The databases do not need to be unpacked or prepared in any way after download.

You can verify that they've been successfully downloaded (and view database properties such as `ksize` and `scaled`) with `sourmash sig summarize <output>`.

## Sketches for human and animal genomes

These include k=21, k=31, and k=51, at a scaled of 1000. Each file is about 110 MB.
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Suggested change
These include k=21, k=31, and k=51, at a scaled of 1000. Each file is about 110 MB.
These signature files are representative sketches of model organisms. There suggested usage is to identify and remove contamination from environmental sketches. These include k=21, k=31, and k=51, at a scaled of 1000. Each file is about 110 MB.

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updated in dc9d435 with:
+These sketches are of the latest releases of a number of animal
+genomes. Among other uses, they can be used to detect host
+contamination in microbial metagenomes.
+
+Each file includes sketches at k=21, k=31, and k=51, at a scaled of
+1000, and is about 110 MB.

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ctb commented Dec 8, 2024

Also, would you like to add some of the more canonical organisms? Namely,

  1. rat https://www.ncbi.nlm.nih.gov/datasets/taxonomy/10116/

  2. xenopus https://www.ncbi.nlm.nih.gov/datasets/taxonomy/8355/

  3. zebrafish https://www.ncbi.nlm.nih.gov/datasets/taxonomy/7955/

  4. drosophila https://ncbi.nlm.nih.gov/datasets/taxonomy/7227/

  5. c. elegans https://www.ncbi.nlm.nih.gov/datasets/taxonomy/6239/

No, I just want to merge ;).

I've added these to #2717 so we don't lose the suggestion. But the pipeline I'm using doesn't do anything fancy and I don't want to piecemeal add new genomes (because it's work, and it's also error prone ;) until we automated the process more.

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LGTM

@ctb ctb merged commit 7e744e7 into latest Dec 8, 2024
42 of 44 checks passed
@ctb ctb deleted the add_animal_sketches branch December 8, 2024 16:55
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2 participants