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.
Taxonomic Information (for non-LCA databases)¶
For each prepared database, we have also made taxonomic information available linking each genome with its assigned lineage (GTDB or NCBI as appropriate).
For private databases, users can create their own taxonomy files: the critical columns are ident, containing the genome accession (e.g. GCA_1234567.1) and
a column for each taxonomic rank, superkingdom to species. If a strain column is provided, it will also be used.
As of v4.8, we can also use LIN taxonomic information in tax commands that accept the --lins flag. If used, sourmash tax commands will require a lin column in the taxonomy file which should contain ;-separated LINs, preferably with a standard number of positions (e.g. all 20 positions in length or all 10 positions in length). Some taxonomy commands also accept a lingroups file, which is a two-column file (name, lin) describing the name and LIN prefix of LINgroups to be used for taxonomic summarization.
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 R08-RS214 - DNA databases¶
GTDB R08-RS214 consists of 402,709 genomes organized into 85,205 species clusters.
The lineage spreadsheet (for sourmash tax commands) is available at the species level.
GTDB R08-RS214 genomic representatives (85k)¶
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 |
|||
31 |
|||
51 |
GTDB R08-RS214 all genomes (403k)¶
These are databases for the full GTDB release, each containing 402,709 genomes.
K-mer size |
Zipfile collection |
SBT |
LCA |
|---|---|---|---|
21 |
|||
31 |
|||
51 |
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 archaeal¶
8,750 genomes:
genbank-2022.03-archaea-k21.zip
genbank-2022.03-archaea-k31.zip
Genbank protozoa¶
1193 genomes:
genbank-2022.03-protozoa-k21.zip
genbank-2022.03-protozoa-k31.zip
Genbank fungi¶
10,286 genomes:
Genbank bacterial:¶
1,148,011 genomes:
genbank-2022.03-bacteria-k21.zip
genbank-2022.03-bacteria-k31.zip
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 genome 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 |
|||
31 |
|||
51 |
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 |
|||
31 |
|||
51 |
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 |
|||
31 |
|||
51 |
GTDB R06-RS202 all genomes (258k)¶
These databases contain the complete GTDB collection of 258,406 genomes.
K-mer size |
Zipfile collection |
SBT |
LCA |
|---|---|---|---|
21 |
|||
31 |
|||
51 |
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
lcasubcommands 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.
