Accessing and downloading data#

The mOTUs-db provides access to genome, gene, and protein sequences, and annotations for nearly 4 million genomes. These are licensed under CC BY 4.0 and freely accessible via the online interface, the mOTUs API and the motus genomes and motus download commands of the mOTUs command-line tool.

For more usage instructions, see the interface navigation guide, the mOTUs API page and the tutorial for motus genomes and motus download commands.

When should I use the online interface?#

The online interface is the most accessible way to navigate the dataset and uniquely allows users to filter genomes by quality, GC content, and genome size. After navigating to the individual genome page, e.g. ELLE19-1_SAMN09288280_MAG_00000004, the user can download all files associated with this genome. The online interface can also be used to generate and download a table containing genome identifiers of interest via the Export Metadata button on the genome overview page. This list of genome identifiers can then be used for bulk downloads through the API.

When should I use the API?#

The API enables bulk downloads and is also used by the motus download command of the command-line tool. For parallel downloads, we recommend using the API.

When should I use the command-line tool?#

The mOTUs command-line tool enables the user to search for genomes based on any taxonomic (e.g. Gilliamella) or (uniquely) functional group (e.g. K12743) annotations with motus genomes. The output of the motus genomes command can then be passed directly into the motus download command. Alternatively, the list of genome identifiers in the output can be used for bulk downloads through the API.

Gene catalogs#

The gene catalogs represent clusters generated at different identity levels in nucleotide space, encompassing all genes found in the mOTUs 4.1 genomes. They can be downloaded from the FTP server.

mOTUs Gene Catalog Statistics#

Name

# Clusters

Cutoff

Singletons

Sequences

Clusters

mOTUsv4.1_NT_G_NR100

2,311,507,841

100

1,823,363,474

mOTUsv4.1_NT_G_NR100.fna.gz

mOTUsv4.1_NT_G_NR100.tsv.gz

mOTUsv4.1_NT_G_NR95

481,546,886

95

268,400,540

mOTUsv4.1_NT_G_NR95.fna.gz

mOTUsv4.1_NT_G_NR95.tsv.gz

Supplementary files#

All supplementary files for mOTUs-db can be found on the mOTUs Zenodo Community.

ico1 mOTUs is part of SIB's portfolio of open tools and databases.

ico2 mOTUs is part of the ELIXIR-CH Service Delivery Plan.