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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Vydáno v:Bioinformatics (Oxford, England) Ročník 38; číslo 23; s. 5315 - 5316
Hlavní autoři: Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 30.11.2022
Témata:
Applications Note
Documentation
Software
ISSN:1367-4803, 1367-4811, 1367-4811
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btac672