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...

Celý popis

Uložené v:
Podrobná bibliografia
Vydané v:Bioinformatics (Oxford, England) Ročník 38; číslo 23; s. 5315 - 5316
Hlavní autori: Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Oxford University Press 30.11.2022
Predmet:
Applications Note
Documentation
Software
ISSN:1367-4803, 1367-4811, 1367-4811
On-line prístup:Získať plný text
Tagy: Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
Popis
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.
Bibliografia: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