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MRG: add genbank plant db to docs #3429

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merged 3 commits into from
Dec 16, 2024
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MRG: add genbank plant db to docs #3429

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cf19c13
add plant db
bluegenes Dec 10, 2024
1facf5b
fix file sizes for host genomes, too
ctb Dec 14, 2024
60802f6
Merge branch 'latest' into plant-db
bluegenes Dec 16, 2024
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14 changes: 13 additions & 1 deletion doc/databases.md
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Expand Up @@ -37,7 +37,7 @@ 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.
1000, and is under 50 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)
Expand All @@ -49,6 +49,18 @@ Each file includes sketches at k=21, k=31, and k=51, at a scaled of
* 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)

## Sketches for plant genomes

These sketches are for the plant genomes available in GenBank as of 2024-07.

| K-mer size | Zipfile collection |
| -------- | -------- |
| k21 | [download (7G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k21.zip) |
| k31 | [download (8.8G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k31.zip) |
| k51 | [download (11G)](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.k51.zip) |

Lineage spreadsheet for sourmash `tax` commands: [download](https://farm.cse.ucdavis.edu/\~ctbrown/sourmash-db/genbank-plant-2024-07/genbank-plants-2024-07.lineages.csv.gz)

## 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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