| title | description | published | date | tags | editor | dateCreated |
|---|---|---|---|---|---|---|
Genome Taxonomy Database |
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny. |
true |
2020-09-11 14:11:42 UTC |
2018, taxonomy, phylogeny, database, 2020 |
markdown |
2020-05-27 18:16:59 UTC |
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarly funded by an Australian Research Council Laureate Fellowship.
The genomes used to construct the phylogeny are obtained from RefSeq and Genbank, and GTDB releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB. {.is-info}
- GTDB Main Page {.links-list}
- Link to related tools.
- Downloadable content.
- Statistic available.
- Can explore on the tree of life or search organism name or NCBI number.
- Lots of different informaions of the strain page.
- Help section FAQ
- Help section Forum {.links-list}
- Parks, D. H., Chuvochina, M., Chaumeil, P. A., Rinke, C., Mussig, A. J., & Hugenholtz, P. (2020). A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology, 1-8.
- Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P. A., & Hugenholtz, P. (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature biotechnology, 36(10), 996-1004.
- Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. {.grid-list}