GlobDB & other custom resources

GlobDB - There is no paper that is appropriate to cite for the GlobDB. For now, please just cite the website if you use the resource.

CUGO -  There is no paper that describes the concensus genomic context approach yet.

Data sources

genome taxonomy database (GTDB) - The GTDB website provides a complete list of references to cite here. The most recent publication for the GTDB is Parks et al. 2022.

genomic catalog of earth's microbiomes (GEM) -The GEM species representatives (as species-level OTUs) are described in Roux et al. 2021.

searchable, planetary-scale microbiome resource (SPIRE) - The SPIRE and SPECI species representatives (as species-level clusters) are described in Schmidt et al. 2023.

genomic catalog of soil microbiomes (SMAG) - The SMAG species representatives (as species-level genome bins) are described in Ma et al. 2023.

Tools

fastANI - Dereplication of the datasets is done using fastANI, version 1.3.4, described in Jain et al. 2018.

Anvi'o - Anvi'o contigs databases for the GlobDB genomes, as well as the protein files and GFF files were created using anvi'o, development version, described in Eren et al. 2021. In addition, anvi'o provides a wide range of functionalities, some of which come with their own citations. If you use the GlobDB anvi'o databases in your work please check here whether there's work that would be appropriate to cite. 

Prodigal - The proteins in the GlobDB genomes were annotated using Prodigal, version 2.6.3, described in Hyatt et al. 2010. If you use the protein data files in your work consider citing prodigal.

GTDB-tk - The taxonomy for the genomes in the GlobDB that are not derived from the GTDB is assigned using GTDB-tk, version 2.4.0, described in Chaumeil et al. 2022.

TMHMM - Transmembrane helices were predicted in the GlobDB genomes using TMHMM, version 2.0c, described in Krogh et al. 2001.

BBTools - statistics on the GlobDB genomes were calculated using the statswrapper.sh script that comes with the BBMap package. To the best of my knowledge there is no publication describing BBMap.