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# Collection: NCBI Viruses (Jan 2025)

All viruses from NCBI (NCBI:txid10239) as of January 2025.

Links:

* [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=10239&lvl=3&lin=f&keep=1&srchmode=1&unlock)

## Database files


### Zip collections

   * zip: [ncbi-viruses-2025.01.dna.k=21.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=21.sig.zip) - all viral genomes - DNA, k=21, scaled=50 (1.4 GB)

   * zip: [ncbi-viruses-2025.01.dna.k=31.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=31.sig.zip) - all viral genomes - DNA, k=31, scaled=50 (1.4 GB)

   * zip: [ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip) - all viral genomes - skip_m2n3, k=24, scaled=50 (2.7 GB)


## Taxonomy files

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


## Advanced

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### Complete list of database files

Files:

* zip: [ncbi-viruses-2025.01.dna.k=21.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=21.sig.zip) - all viral genomes - DNA, k=21, scaled=50 (1.4 GB)
* zip: [ncbi-viruses-2025.01.dna.k=31.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=31.sig.zip) - all viral genomes - DNA, k=31, scaled=50 (1.4 GB)
* zip: [ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip) - all viral genomes - skip_m2n3, k=24, scaled=50 (2.7 GB)


### Download via curl using the command line

```shell
# download ncbi-viruses-2025.01.dna.k=21.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=21.sig.zip

# download ncbi-viruses-2025.01.dna.k=31.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=31.sig.zip

# download ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip

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


### A list of all the URLs

```
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=21.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=31.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.skip_m2n3.k=24.sig.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses.2025.01.lineages.csv
```