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Collection: GTDB RS226

Bacterial and Archaeal genomes from GTDB RS226.

Links:

Database files

K-mer size GTDB reps GTDB entire RocksDB index of entire
21 download (3.7 GB) download (21.0 GB) download (31.0 GB)
31 download (3.7 GB) download (21.0 GB) download (32.0 GB)
51 download (3.7 GB) download (21.0 GB) download (33.0 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 in order to avoid temporarily using disk space to store the downloaded tar.gz.

Taxonomy files

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Complete list of database files

Files:

Download via curl using the command line

# download gtdb-reps-rs226-k21.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k21.dna.zip

# download gtdb-reps-rs226-k31.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k31.dna.zip

# download gtdb-reps-rs226-k51.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k51.dna.zip

# download gtdb-rs226-k21.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip

# download gtdb-rs226-k31.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip

# download gtdb-rs226-k51.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip

# download gtdb-rs226-k21.dna.rocksdb.tar.gz
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz

# download gtdb-rs226-k31.dna.rocksdb.tar.gz
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz

# download gtdb-rs226-k51.dna.rocksdb.tar.gz
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz

# download taxonomy file
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv

Download and unpack RocksDB indexes


# download and unpack gtdb-rs226-k21.dna.rocksdb.tar.gz
curl -L https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz | tar xzf -

# download and unpack gtdb-rs226-k31.dna.rocksdb.tar.gz
curl -L https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz | tar xzf -

# download and unpack gtdb-rs226-k51.dna.rocksdb.tar.gz
curl -L https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz | tar xzf -

A list of all the URLs

https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k21.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k31.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k51.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv