Collection: GTDB RS220¶
Bacterial and Archaeal genomes from GTDB RS220.
Links:
Database files¶
| K-mer size | GTDB reps | GTDB entire |
|---|---|---|
| 21 | download (2.8 GB) | download (17.0 GB) |
| 31 | download (2.8 GB) | download (17.0 GB) |
| 51 | download (2.8 GB) | download (17.0 GB) |
Taxonomy files¶
Advanced¶
Complete list of database files¶
Files:
- zip: gtdb-rs220-k21.dna.zip - all GTDB genomes - DNA, k=21, scaled=1000 (17.0 GB)
- zip: gtdb-rs220-k31.dna.zip - all GTDB genomes - DNA, k=31, scaled=1000 (17.0 GB)
-
zip: gtdb-rs220-k51.dna.zip - all GTDB genomes - DNA, k=51, scaled=1000 (17.0 GB)
-
zip: gtdb-reps-rs220-k21.dna.zip - GTDB species representative genomes - DNA, k=21, scaled=1000 (2.8 GB)
- zip: gtdb-reps-rs220-k31.dna.zip - GTDB species representative genomes - DNA, k=31, scaled=1000 (2.8 GB)
- zip: gtdb-reps-rs220-k51.dna.zip - GTDB species representative genomes - DNA, k=51, scaled=1000 (2.8 GB)
Download via curl using the command line¶
# download gtdb-rs220-k21.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k21.dna.zip
# download gtdb-rs220-k31.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k31.dna.zip
# download gtdb-rs220-k51.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k51.dna.zip
# download gtdb-reps-rs220-k21.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k21.dna.zip
# download gtdb-reps-rs220-k31.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k31.dna.zip
# download gtdb-reps-rs220-k51.dna.zip
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k51.dna.zip
# download taxonomy file
curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220.lineages.csv
A list of all the URLs¶
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k21.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k31.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k51.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k21.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k31.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k51.dna.zip
https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220.lineages.csv