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[MRG] update the databases page with GTDB R07-RS207 and Genbank 2022.03 #2013

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merged 5 commits into from
May 2, 2022

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@ctb ctb commented Apr 30, 2022

This updates the "prepared databases" page with the new GTDB and the March 2022 Genbank genomes.

Closes #1941 🎉

Both the GTDB and Genbank updates were built with the database-releases code here.

The Genbank taxonomy was built from assembly_summary files using these scripts.

View the updated databases page HERE.

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codecov bot commented Apr 30, 2022

Codecov Report

Merging #2013 (a3ec8a6) into latest (38ebe4e) will increase coverage by 7.52%.
The diff coverage is n/a.

❗ Current head a3ec8a6 differs from pull request most recent head 8a59ea4. Consider uploading reports for the commit 8a59ea4 to get more accurate results

@@            Coverage Diff             @@
##           latest    #2013      +/-   ##
==========================================
+ Coverage   84.14%   91.66%   +7.52%     
==========================================
  Files         129       98      -31     
  Lines       15082    10802    -4280     
  Branches     2118     2118              
==========================================
- Hits        12691     9902    -2789     
+ Misses       2095      604    -1491     
  Partials      296      296              
Flag Coverage Δ
python 91.66% <ø> (ø)
rust ?

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Impacted Files Coverage Δ
src/core/src/sketch/nodegraph.rs
src/core/src/ffi/cmd/compute.rs
src/core/src/ffi/storage.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/ffi/signature.rs
src/core/src/index/sbt/mod.rs
src/core/tests/test.rs
src/core/src/signature.rs
src/core/src/index/search.rs
src/core/src/ffi/mod.rs
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ctb commented Apr 30, 2022

Ready for review and merge @sourmash-bio/devs !

I would rather not do more actual work per se, so if you have ideas for different/additional databases or information we should provide, please put them in an issue (maybe #970, or a new issue). But it's totally fair game to suggest rearranging content or updating the formatting or changing words!

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looking good.

I think it needs some minimal info on scaled -- suggested some additions. Are all databases here scaled=1000, or are the lca/genbank at lower resolution?

doc/databases.md Outdated Show resolved Hide resolved
doc/databases.md Outdated Show resolved Hide resolved
Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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ctb commented May 2, 2022

looking good.

I think it needs some minimal info on scaled -- suggested some additions. Are all databases here scaled=1000, or are the lca/genbank at lower resolution?

See Appendix section ;).

(LCA is at 10k, rest are at 1000.)

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ctb commented May 2, 2022

ok, revised wording appropriately. Should be ready for review!

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lgtm!

@ctb ctb merged commit d425f6f into latest May 2, 2022
@ctb ctb deleted the update/databases branch May 2, 2022 16:39
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release new GTDB databases for R07-RS207
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