The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
Open accessAbstract
Summary: The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB) which limits its adoption and ease of use. Here, we present an update to GTDB-Tk that uses a divide-and-conquer approach where user genomes are initially placed into a bacterial reference tree with family-level representatives followed by placement into an appropriate class-level subtree comprising species representatives. This substantially reduces the memory requirements of GTDB-Tk while having minimal impact on classification. Availability and implementation: GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz848 · Cited by 5,259
Self-citationParks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402
Self-citationA complete domain-to-species taxonomy for Bacteria and Archaea
Parks, D. H., Chuvochina, M., Chaumeil, P.-A., Rinke, C., Mussig, A. J., & Hugenholtz, P. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0501-8 · Cited by 1,530
Self-citationA unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367
Self-citationMatsen, F. A., Kodner, R. B., & Armbrust, E. V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-538 · Cited by 1,050
A genomic catalog of Earth’s microbiomes
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I.-M., Huntemann, M., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0718-6 · Cited by 865
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
Barbera, P., Kozlov, A. M., Czech, L., Morel, B., Darriba, D., Flouri, T., & Stamatakis, A. (2019) · Systematic Biology · doi:10.1093/sysbio/syy054 · Cited by 687
Fast and accurate distance‐based phylogenetic placement using divide and conquer
Balaban, M., Jiang, Y., Roush, D., Zhu, Q., & Mirarab, S. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13527 · Cited by 41
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Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes
Riesco, R., & Trujillo, M. E. (2024) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.006300 · Cited by 579
Camargo, A. P., Nayfach, S., Chen, I.-M. A., Palaniappan, K., Ratner, A., Chu, K., Ritter, S. J., Reddy, T. B. K., Mukherjee, S., Schulz, F., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1037 · Cited by 446
A gut microbial signature for combination immune checkpoint blockade across cancer types
Gunjur, A., Shao, Y., Rozday, T., Klein, O., Mu, A., Haak, B. W., Markman, B., Kee, D., Carlino, M. S., Underhill, C., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-02823-z · Cited by 165
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad964 · Cited by 87
Peng, Y., Lu, Z., Pan, D., Shi, L.-D., Zhao, Z., Liu, Q., Zhang, C., Jia, K., Li, J., Hubert, C. R. J., et al. (2023) · The ISME Journal · doi:10.1038/s41396-023-01491-0 · Cited by 48
Metadata
- Authors
- Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-10-11
- Volume
- 38
- Issue
- 23
- Pages
- 5315-5316
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W4304481015
- Cited by
- 2,061
- References
- 8
- FWCI
- 92.60
- Type
- journal article
- Language
- en
- Open access
- hybrid
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