Prepared databases

We provide a number of pre-built collections and indexed databases that you can use with sourmash.

Types of databases

For each k-mer size, three types of databases may be available: Zipfile (.zip), SBT (.sbt.zip), and LCA (.lca.jzon.gz). The Zipfile and SBT databases are built with scaled=1000, and then LCA databases are built with scaled=10,000. We recommend using the Zipfile databases for sourmash gather and the SBT databases for sourmash search. You must use the LCA databases for sourmash lca operations.

You can read more about the different database and index types here.

Note that the SBT and LCA databases can be used with sourmash v3.5 and later, while Zipfile collections can only be used with sourmash v4.1 and up.

Downloading and using the databases

All databases below can be downloaded via the command line with curl -JLO <url>, where <url> is the URL below. This will download an appropriately named file; you can name it yourself by specify '-o <output> to specify the local filename.

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 R07-RS207 consists of 317,542 genomes organized into 65,703 species clusters.

The lineage spreadsheet (for sourmash tax commands) is available at the species level and at the strain level.

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)

download (3.5 GB)

download (181 MB)

31

download (1.7 GB)

download (3.5 GB)

download (181 MB)

51

download (1.7 GB)

download (3.5 GB)

download (181 MB)

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)

download (19 GB)

download (351 MB)

31

download (9.4 GB)

download (19 GB)

download (351 MB)

51

download (9.4 GB)

download (19 GB)

download (351 MB)

Genbank genomes from March 2022

The below zip files contain different subsets of the signatures for all microbial Genbank genomes. The databases were built in March 2022, and are based on the assembly_summary files provided here.

Since some of the files are extremely large, we only provide them in Zip format (which is our smallest and most flexible format).

Note that all of the sourmash search commands support multiple databases on the command line, so you can search multiple subsets simply by providing them all on the command line, e.g. sourmash search query.sig genbank-2022.03-{viral,protozoa}-k31.zip.

Taxonomic spreadsheets for each domain are provided below as well.

Genbank viral

47,952 genomes:

genbank-2022.03-viral-k21.zip

genbank-2022.03-viral-k31.zip

genbank-2022.03-viral-k51.zip

genbank-2022.03-viral.lineages.csv.gz

Genbank archaeal

8,750 genomes:

genbank-2022.03-archaea-k21.zip

genbank-2022.03-archaea-k31.zip

genbank-2022.03-archaea-k51.zip

genbank-2022.03-archaea.lineages.csv.gz

Genbank protozoa

1193 genomes:

genbank-2022.03-protozoa-k21.zip

genbank-2022.03-protozoa-k31.zip

genbank-2022.03-protozoa-k51.zip

genbank-2022.03-protozoa.lineages.csv.gz

Genbank fungi

10,286 genomes:

genbank-2022.03-fungi-k21.zip

genbank-2022.03-fungi-k31.zip

genbank-2022.03-fungi-k51.zip

genbank-2022.03-fungi.lineages.csv.gz

Genbank bacterial:

1,148,011 genomes:

genbank-2022.03-bacteria-k21.zip

genbank-2022.03-bacteria-k31.zip

genbank-2022.03-bacteria-k51.zip

genbank-2022.03-bacteria.lineages.csv.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.

GTDB R06-RS202 genomic representatives (47.8k)

The GTDB genomic representatives are a low-redundancy subset of Genbank genomes.

K-mer size

Zipfile collection

SBT

LCA

21

download (1.3 GB)

download (2.6 GB)

download (114 MB)

31

download (1.3 GB)

download (2.6 GB)

download (131 MB)

51

download (1.3 GB)

download (2.6 GB)

download (137 MB)

GTDB all genomes (258k)

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

K-mer size

Zipfile collection

SBT

LCA

21

download (7.8 GB)

download (15 GB)

download (266 MB)

31

download (7.8 GB)

download (15 GB)

download (286 MB)

51

download (7.8 GB)

download (15 GB)

download (299 MB)

Appendix: database use and construction details

Database release workflows are being archived at sourmash-bio/database-releases.

Some more details on database use and construction:

  • Zipfile collections can be used for a linear search. The signatures were calculated with a scaled of 1000, which robustly supports searches for ~10kb or larger matches.

  • SBT databases are indexed versions of the Zipfile collections that support faster search. They are also indexed with scaled=1000.

  • LCA databases are indexed versions of the Zipfile collections that also contain taxonomy information and can be used with regular search as well as with the lca subcommands for taxonomic analysis. They are indexed with scaled=10,000, which robustly supports searches for 100kb or larger matches.

Appendix: Memory and time requirements

The detailed memory usage of sourmash depends on the type of search, the query, and the database you’re searching, but to help guide you here is a range of numbers:

Search type

Query

Database

Max RAM

Time

gather

Bacterial genome

GTDB complete (280k)

1 GB

6 minutes

gather

Simple metagenome

GTDB reps .zip (65k)

2 GB

6 minutes

gather

Real metagenome

All Genbank (1.2m)

100 GB

3 hours

lca summarize

Simple metagenome

GTDB reps .sql (65k)

400 MB

20 seconds

lca summarize

Simple metagenome

GTDB reps .json (65k)

6.2 GB

1m 20 seconds

Please see sourmash#1958 for detailed GTDB numbers and gather paper#47 for detailed Genbank numbers.

Appendix: legacy databases

Legacy databases are available here.