GTDB-Tk v2: memory friendly classification with the genome taxonomy database
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...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) Jg. 38; H. 23; S. 5315 - 5316 |
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| Hauptverfasser: | , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
Oxford University Press
30.11.2022
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| Schlagworte: | |
| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
| Online-Zugang: | Volltext |
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| Zusammenfassung: | 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.
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 data are available at Bioinformatics online. |
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| Bibliographie: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISSN: | 1367-4803 1367-4811 1367-4811 |
| DOI: | 10.1093/bioinformatics/btac672 |