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Merge pull request #3 from sourmash-bio/update_tables
MRG: update with tables and other trickery
2 parents ddd6eb4 + 5cd701b commit fc881e2

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‎Snakefile‎

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@@ -7,16 +7,16 @@ Templates_To_Output = namedtuple("Templates_To_Output",
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templates = [
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Templates_To_Output('gtdb220',
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'complete',
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'gtdb',
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'outputs/md/gtdb220.md'),
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Templates_To_Output('gtdb226',
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'complete',
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'gtdb+rocksdb',
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'outputs/md/gtdb226.md'),
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Templates_To_Output('ncbi_viruses_2025_01',
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'complete',
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'ncbi',
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'outputs/md/ncbi_viruses_2025_01.md'),
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Templates_To_Output('ncbi_euks_2025_01',
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'complete',
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'ncbi',
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'outputs/md/ncbi_euks_2025_01.md'),
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]
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‎outputs/md/gtdb220.md‎

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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/complete.md -->
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<!-- template file: templates/gtdb.md -->
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# Collection: GTDB RS220
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## Database files:
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Files:
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| K-mer size | GTDB reps | GTDB entire |
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| -------- | -------- | -------- |
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| 21 | [download (2.8 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k21.dna.zip) | [download (17.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k21.dna.zip) |
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| 31 | [download (2.8 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k31.dna.zip) | [download (17.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k31.dna.zip) |
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| 51 | [download (2.8 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k51.dna.zip) | [download (17.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k51.dna.zip) |
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* zip: [gtdb-rs220-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k21.dna.zip) - all GTDB genomes. - DNA, k=21, scaled=1000 (17.0 GB)
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* zip: [gtdb-rs220-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k31.dna.zip) - all GTDB genomes. - DNA, k=31, scaled=1000 (17.0 GB)
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* zip: [gtdb-rs220-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k51.dna.zip) - all GTDB genomes. - DNA, k=51, scaled=1000 (17.0 GB)
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## Taxonomy files:
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* zip: [gtdb-reps-rs220-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k21.dna.zip) - all GTDB species representative genomes. - DNA, k=21, scaled=1000 (2.8 GB)
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* zip: [gtdb-reps-rs220-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k31.dna.zip) - all GTDB species representative genomes. - DNA, k=31, scaled=1000 (2.8 GB)
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* zip: [gtdb-reps-rs220-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k51.dna.zip) - all GTDB species representative genomes. - DNA, k=51, scaled=1000 (2.8 GB)
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* [GTDB taxonomy for RS220.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220.lineages.csv)
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## Advanced
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## Taxonomy files:
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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/advanced.md -->
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* [GTDB taxonomy for RS220.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220.lineages.csv)
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### Complete list of database files
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Files:
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* zip: [gtdb-rs220-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k21.dna.zip) - all GTDB genomes - DNA, k=21, scaled=1000 (17.0 GB)
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* zip: [gtdb-rs220-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k31.dna.zip) - all GTDB genomes - DNA, k=31, scaled=1000 (17.0 GB)
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* zip: [gtdb-rs220-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-rs220-k51.dna.zip) - all GTDB genomes - DNA, k=51, scaled=1000 (17.0 GB)
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* zip: [gtdb-reps-rs220-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k21.dna.zip) - GTDB species representative genomes - DNA, k=21, scaled=1000 (2.8 GB)
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* zip: [gtdb-reps-rs220-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k31.dna.zip) - GTDB species representative genomes - DNA, k=31, scaled=1000 (2.8 GB)
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* zip: [gtdb-reps-rs220-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs220/gtdb-reps-rs220-k51.dna.zip) - GTDB species representative genomes - DNA, k=51, scaled=1000 (2.8 GB)
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## Advanced
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### Download via curl using the command line
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‎outputs/md/gtdb226.md‎

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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/complete.md -->
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<!-- template file: templates/gtdb.md -->
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# Collection: GTDB RS226
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## Database files:
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Files:
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| K-mer size | GTDB reps | GTDB entire | RocksDB index of entire |
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| -------- | -------- | -------- | ---- |
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| 21 | [download (3.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k21.dna.zip) | [download (21.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip) | [download (31.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.zip) |
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| 31 | [download (3.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k31.dna.zip) | [download (21.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip) | [download (32.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.zip) |
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| 51 | [download (3.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k51.dna.zip) | [download (21.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip) | [download (33.0 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.zip) |
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* zip: [gtdb-reps-rs226-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k21.dna.zip) - all GTDB species representative genomes. - DNA, k=21, scaled=1000 (21.0 GB)
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* zip: [gtdb-reps-rs226-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k31.dna.zip) - all GTDB species representative genomes. - DNA, k=31, scaled=1000 (21.0 GB)
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* zip: [gtdb-reps-rs226-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k51.dna.zip) - all GTDB species representative genomes. - DNA, k=51, scaled=1000 (21.0 GB)
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Note: RocksDB indexes must be unzipped before use, while the other
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databases can be used directly as zip files.
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* zip: [gtdb-rs226-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip) - all GTDB genomes - DNA, k=21, scaled=1000 (21.0 GB)
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* zip: [gtdb-rs226-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip) - all GTDB genomes - DNA, k=31, scaled=1000 (21.0 GB)
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* zip: [gtdb-rs226-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip) - all GTDB genomes - DNA, k=51, scaled=1000 (21.0 GB)
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## Taxonomy files:
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* [GTDB taxonomy for RS226.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv)
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* tar.gz: [gtdb-rs226-k21.dna.rocksdb.tar.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz) - all GTDB genomes, indexed with RocksDB - DNA, k=21, scaled=1000 (31.0 GB)
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* tar.gz: [gtdb-rs226-k31.dna.rocksdb.tar.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz) - all GTDB genomes, indexed with RocksDB - DNA, k=31, scaled=1000 (32.0 GB)
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* tar.gz: [gtdb-rs226-k51.dna.rocksdb.tar.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz) - all GTDB genomes, indexed with RocksDB - DNA, k=51, scaled=1000 (33.0 GB)
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## Advanced
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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/advanced.md -->
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## Taxonomy files:
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### Complete list of database files
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* [GTDB taxonomy for RS226.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv)
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Files:
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* zip: [gtdb-reps-rs226-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k21.dna.zip) - GTDB species representative genomes - DNA, k=21, scaled=1000 (3.7 GB)
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* zip: [gtdb-reps-rs226-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k31.dna.zip) - GTDB species representative genomes - DNA, k=31, scaled=1000 (3.7 GB)
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* zip: [gtdb-reps-rs226-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-reps-rs226-k51.dna.zip) - GTDB species representative genomes - DNA, k=51, scaled=1000 (3.7 GB)
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* zip: [gtdb-rs226-k21.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip) - all GTDB genomes - DNA, k=21, scaled=1000 (21.0 GB)
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* zip: [gtdb-rs226-k31.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip) - all GTDB genomes - DNA, k=31, scaled=1000 (21.0 GB)
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* zip: [gtdb-rs226-k51.dna.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip) - all GTDB genomes - DNA, k=51, scaled=1000 (21.0 GB)
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* tar.gz: [gtdb-rs226-k21.dna.rocksdb.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.zip) - all GTDB genomes, indexed with RocksDB - DNA, k=21, scaled=1000 (31.0 GB)
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* tar.gz: [gtdb-rs226-k31.dna.rocksdb.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.zip) - all GTDB genomes, indexed with RocksDB - DNA, k=31, scaled=1000 (32.0 GB)
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* tar.gz: [gtdb-rs226-k51.dna.rocksdb.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.zip) - all GTDB genomes, indexed with RocksDB - DNA, k=51, scaled=1000 (33.0 GB)
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## Advanced
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### Download via curl using the command line
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# download gtdb-rs226-k51.dna.zip
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip
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# download gtdb-rs226-k21.dna.rocksdb.tar.gz
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz
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# download gtdb-rs226-k21.dna.rocksdb.zip
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.zip
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# download gtdb-rs226-k31.dna.rocksdb.tar.gz
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz
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# download gtdb-rs226-k31.dna.rocksdb.zip
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.zip
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# download gtdb-rs226-k51.dna.rocksdb.tar.gz
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz
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# download gtdb-rs226-k51.dna.rocksdb.zip
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.zip
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# download taxonomy file
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curl -O --no-clobber https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.zip
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https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv
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```

‎outputs/md/ncbi_euks_2025_01.md‎

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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/complete.md -->
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<!-- template file: templates/ncbi.md -->
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# Collection: NCBI Eukaryotes (Jan 2025)
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## Database files:
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Indexed RocksDB collections:
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* zip: [ncbi-euks-all-2025.01.k51.rocksdb.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-euks-2025.01/ncbi-euks-all-2025.01.k51.rocksdb.zip) - all NCBI eukaryotes, indexed in a RocksDB - DNA, k=51, scaled=10000 (19.0 GB)
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Note: RocksDB indexes must be unzipped before use.
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Zip collections:
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* zip: [ncbi-euks-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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* zip: [ncbi-euks-bilateria-minus-vertebrates-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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* zip: [ncbi-euks-plants-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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* zip: [ncbi-euks-fungi-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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* zip: [ncbi-euks-metazoa-minus-bilateria-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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* zip: [ncbi-euks-other-2025.01.dna.k=51.sig.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-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)
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## Taxonomy files:
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* [NCBI taxonomy for eukaryotes (NCBI:txid2759) as of January 2025.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-euks-2025.01/ncbi-eukaryotes.2025.01.lineages.csv)
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## Advanced
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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/advanced.md -->
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### Complete list of database files
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* zip: [ncbi-euks-all-2025.01.k51.rocksdb.zip](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-euks-2025.01/ncbi-euks-all-2025.01.k51.rocksdb.zip) - all NCBI eukaryotes, indexed in a RocksDB - DNA, k=51, scaled=10000 (19.0 GB)
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## Taxonomy files:
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* [NCBI taxonomy for eukaryotes (NCBI:txid2759) as of January 2025.](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/genbank-euks-2025.01/ncbi-eukaryotes.2025.01.lineages.csv)
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## Advanced
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### Download via curl using the command line
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```shell

‎outputs/md/ncbi_viruses_2025_01.md‎

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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/complete.md -->
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<!-- template file: templates/ncbi.md -->
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# Collection: NCBI Viruses (Jan 2025)
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## Database files:
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Files:
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* 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)
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* 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)
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* 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)
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Zip collections:
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* 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)
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* 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)
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* 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)
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## Taxonomy files:
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## Advanced
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<!-- automatically generated by code in https://github.com/sourmash-bio/2025-sourmash-databases-doc-template/ -->
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<!-- template file: templates/advanced.md -->
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### Complete list of database files
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Files:
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* 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)
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* 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)
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* 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)
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### Download via curl using the command line
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```shell

‎outputs/scripts/check-urls.py‎

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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.tar.gz',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.tar.gz',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.tar.gz',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k21.dna.rocksdb.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k31.dna.rocksdb.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226-k51.dna.rocksdb.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/gtdb-rs226/gtdb-rs226.lineages.csv',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=21.sig.zip',
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'https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db.new/ncbi-viruses-2025.01/ncbi-viruses-2025.01.dna.k=31.sig.zip',

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