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MRG: update with misc animal genomes #3422

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Dec 8, 2024
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MRG: update with misc animal genomes #3422

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a864471
update with misc animal genomes
ctb Dec 7, 2024
dc9d435
upd text per colton
ctb Dec 8, 2024
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14 changes: 14 additions & 0 deletions doc/databases.md
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Expand Up @@ -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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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.


* Human (hg38) - [hg38.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/hg38.sig.zip)
* Cow (bosTau9) - [bosTau9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/bosTau9.sig.zip)
* Dog (canFam6) - [canFam6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/canFam6.sig.zip)
* Horse (equCab3) - [equCab3.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/equCab3.sig.zip)
* Cat (felCat9) - [felCat9.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/felCat9.sig.zip)
* Chicken (galGAl6) - [galGal6.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/galGal6.sig.zip)
* Mouse (mm39) - [mm39.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/mm39.sig.zip)
* Goat (oviAri4) - [oviAri4.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/oviAri4.sig.zip)
* Pig (susCr11) - [susScr11.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/host/susScr11.sig.zip)

## GTDB R08-RS214 - DNA databases

[GTDB R08-RS214](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r08-rs214/456) consists of 402,709 genomes organized into 85,205 species clusters.
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