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Collection: NCBI Eukaryotes (Jan 2025)

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

Links:

Database files

Indexed RocksDB collections

Note: RocksDB indexes must be unpacked before use, while the other databases can be used directly as zip files. You can unpack while downloading in order to avoid temporarily using disk space to store the downloaded tar.gz.

Zip collections

Taxonomy files

Advanced

Complete list of database files

Files:

Download via curl using the command line

# 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