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[MRG] add gtdb-rs214 info (#2618)
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Adds database info for dbs generated via
sourmash-bio/database-releases#3
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@bluegenes
bluegenes authored May 23, 2023
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55 changes: 41 additions & 14 deletions doc/databases.md
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Expand Up @@ -30,31 +30,31 @@ The databases do not need to be unpacked or prepared in any way after download.

You can verify that they've been successfully downloaded (and view database properties such as `ksize` and `scaled`) with `sourmash sig summarize <output>`.

## GTDB R07-RS207 - DNA databases
## GTDB R08-RS214 - DNA databases

[GTDB R07-RS207](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r07-rs207/264) consists of 317,542 genomes organized into 65,703 species clusters.
[GTDB R08-RS214](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r08-rs214/456) consists of 402,709 genomes organized into 85,205 species clusters.

The lineage spreadsheet (for `sourmash tax` commands) is available [at the species level](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.species-taxonomy.csv.gz) and [at the strain level](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.taxonomy.with-strain.csv.gz).
The lineage spreadsheet (for `sourmash tax` commands) is available [at the species level](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214.lineages.csv.gz).

### GTDB R07-RS207 genomic representatives (66k)
### GTDB R08-RS214 genomic representatives (85k)

The GTDB genomic representatives are a low-redundancy subset of Genbank genomes, with 65,703 species-level genomes.
The GTDB genomic representatives are a low-redundancy subset of Genbank genomes, with 85,205 species-level genomes.

| K-mer size | Zipfile collection | SBT | LCA |
| -------- | -------- | -------- | ---- |
| 21 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.lca.json.gz) |
| 31 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.lca.json.gz) |
| 51 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.lca.json.gz) |
| 21 | [download (2.2 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k21.zip) | [download (4.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k21.sbt.zip) | [download (189 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207gtdb-rs214-reps.k21.lca.json.gz) |
| 31 | [download (2.2 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k31.zip) | [download (4.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k31.sbt.zip) | [download (221 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-reps.k31.lca.json.gz) |
| 51 | [download (2.2 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k51.zip) | [download (4.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-reps.k51.sbt.zip) | [download (230 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-reps.k51.lca.json.gz) |

### GTDB R07-RS207 all genomes (318k)
### GTDB R08-RS214 all genomes (403k)

These are databases for the full GTDB release, each containing 317,542 genomes.
These are databases for the full GTDB release, each containing 402,709 genomes.

| K-mer size | Zipfile collection | SBT | LCA |
| -------- | -------- | -------- | ---- |
| 21 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.lca.json.gz) |
| 31 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.lca.json.gz) |
| 51 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.lca.json.gz) |
| 21 | [download (12 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k21.zip) | [download (23 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k21.sbt.zip) | [download (406 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k21.lca.json.gz) |
| 31 | [download (12 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k31.zip) | [download (23 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k31.sbt.zip) | [download (438 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k31.lca.json.gz) |
| 51 | [download (12 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k51.zip) | [download (23 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k51.sbt.zip) | [download (460 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs214-k51.lca.json.gz) |

## Genbank genomes from March 2022

Expand Down Expand Up @@ -135,6 +135,33 @@ Taxonomic spreadsheets for each domain are provided below as well.

[genbank-2022.03-bacteria.lineages.csv.gz](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/genbank-2022.03/genbank-2022.03-bacteria.lineages.csv.gz)

## GTDB R07-RS207 - DNA databases

[GTDB R07-RS207](https://forum.gtdb.ecogenomic.org/t/announcing-gtdb-r07-rs207/264) consists of 317,542 genomes organized into 65,703 species clusters.

The lineage spreadsheet (for `sourmash tax` commands) is available [at the species level](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.species-taxonomy.csv.gz) and [at the genome level](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.taxonomy.with-strain.csv.gz).

### GTDB R07-RS207 genomic representatives (66k)

The GTDB genomic representatives are a low-redundancy subset of Genbank genomes, with 65,703 species-level genomes.

| K-mer size | Zipfile collection | SBT | LCA |
| -------- | -------- | -------- | ---- |
| 21 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k21.lca.json.gz) |
| 31 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k31.lca.json.gz) |
| 51 | [download (1.7 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.zip) | [download (3.5 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.sbt.zip) | [download (181 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic-reps.dna.k51.lca.json.gz) |

### GTDB R07-RS207 all genomes (318k)

These are databases for the full GTDB release, each containing 317,542 genomes.

| K-mer size | Zipfile collection | SBT | LCA |
| -------- | -------- | -------- | ---- |
| 21 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k21.lca.json.gz) |
| 31 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k31.lca.json.gz) |
| 51 | [download (9.4 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.zip) | [download (19 GB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.sbt.zip) | [download (351 MB)](https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs207/gtdb-rs207.genomic.k51.lca.json.gz) |


## GTDB R06-RS202 - DNA databases

All files below are available under https://osf.io/wxf9z/. The GTDB taxonomy spreadsheet (in a format suitable for `sourmash lca index`) is available [here](https://osf.io/p6z3w/).
Expand All @@ -149,7 +176,7 @@ The GTDB genomic representatives are a low-redundancy subset of Genbank genomes.
| 31 | [download (1.3 GB)](https://osf.io/nqmau/download) | [download (2.6 GB)](https://osf.io/w4bcm/download) | [download (131 MB)](https://osf.io/ypsjq/download) |
| 51 | [download (1.3 GB)](https://osf.io/px6qd/download) | [download (2.6 GB)](https://osf.io/rv9zp/download) | [download (137 MB)](https://osf.io/297dp/download) |

### GTDB all genomes (258k)
### GTDB R06-RS202 all genomes (258k)

These databases contain the complete GTDB collection of 258,406 genomes.

Expand Down

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