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# Collection: NCBI Eukaryotes (Jan 2025)

All eukaryotic reference genomes from NCBI (NCBI:txid2759) as of January 2025.

Links:

* [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2759&lvl=3&lin=f&keep=1&srchmode=1&unlock)

## Database files


### Indexed RocksDB collections

   * tar.gz: [ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz) - all NCBI eukaryotes, indexed in a RocksDB - DNA, k=51, scaled=10000 (19.0 GB)


Note: RocksDB indexes must be unpacked before use, while the other
databases can be used directly as zip files. You can
[unpack while downloading](https://unix.stackexchange.com/questions/85194/how-to-download-an-archive-and-extract-it-without-saving-the-archive-to-disk/85195#85195)
in order to avoid temporarily using disk space to store the downloaded tar.gz.


### Zip collections

   * zip: [ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip) - vertebrate reference genomes (NCBI:txid7742) - DNA, k=51, scaled=10000 (4.0 GB)

   * zip: [ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip) - bilateria minus the vertebrates - DNA, k=51, scaled=10000 (1.7 GB)

   * zip: [ncbi-euks-plants-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-plants-2025.01.dna.k=51.sig.zip) - plant reference genomes (NCBI:txid33090) - DNA, k=51, scaled=10000 (1.3 GB)

   * zip: [ncbi-euks-fungi-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-fungi-2025.01.dna.k=51.sig.zip) - fungal reference genomes (NCBI:txid4751) - DNA, k=51, scaled=10000 (0.2 GB)

   * zip: [ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip) - metazoan reference genomes minus the bilateria - DNA, k=51, scaled=10000 (0.1 GB)

   * zip: [ncbi-euks-other-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-other-2025.01.dna.k=51.sig.zip) - remaining eukaryotes (not plants, fungi, or metazoa) - DNA, k=51, scaled=10000 (0.1 GB)


## Taxonomy files

* [NCBI taxonomy for eukaryotes (NCBI:txid2759) as of January 2025.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-eukaryotes.2025.01.lineages.csv)


## Advanced

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### Complete list of database files

Files:

* tar.gz: [ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz) - all NCBI eukaryotes, indexed in a RocksDB - DNA, k=51, scaled=10000 (19.0 GB)


* zip: [ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip) - vertebrate reference genomes (NCBI:txid7742) - DNA, k=51, scaled=10000 (4.0 GB)


* zip: [ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip) - bilateria minus the vertebrates - DNA, k=51, scaled=10000 (1.7 GB)


* zip: [ncbi-euks-plants-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-plants-2025.01.dna.k=51.sig.zip) - plant reference genomes (NCBI:txid33090) - DNA, k=51, scaled=10000 (1.3 GB)


* zip: [ncbi-euks-fungi-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-fungi-2025.01.dna.k=51.sig.zip) - fungal reference genomes (NCBI:txid4751) - DNA, k=51, scaled=10000 (0.2 GB)


* zip: [ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip) - metazoan reference genomes minus the bilateria - DNA, k=51, scaled=10000 (0.1 GB)


* zip: [ncbi-euks-other-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-other-2025.01.dna.k=51.sig.zip) - remaining eukaryotes (not plants, fungi, or metazoa) - DNA, k=51, scaled=10000 (0.1 GB)


### Download via curl using the command line

```shell
# download ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz

# download ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip

# download ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip

# download ncbi-euks-plants-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-plants-2025.01.dna.k=51.sig.zip

# download ncbi-euks-fungi-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-fungi-2025.01.dna.k=51.sig.zip

# download ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip

# download ncbi-euks-other-2025.01.dna.k=51.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-other-2025.01.dna.k=51.sig.zip

# download taxonomy file
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-eukaryotes.2025.01.lineages.csv
```


### Download and unpack RocksDB indexes

```

# download and unpack ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz
curl -L https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz | tar xzf -

```


### A list of all the URLs

```
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-all-2025.01-k51.dna.rocksdb.tar.gz
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-plants-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-fungi-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-euks-other-2025.01.dna.k=51.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-euks-2025.01/ncbi-eukaryotes.2025.01.lineages.csv
```