Dataset Information

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

ABSTRACT: The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes. GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary data are available at Bioinformatics online.

SUBMITTER: Chaumeil PA

PROVIDER: S-EPMC7703759 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Chaumeil Pierre-Alain PA Mussig Aaron J AJ Hugenholtz Philip P Parks Donovan H DH

Bioinformatics (Oxford, England) 20191115

<h4>Summary</h4>The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes.<h4>Availability</h4>GTDB-Tk is implement ...[more]

PMID: 31730192

Similar Datasets

Project description:BackgroundThis article addresses the problem of interoperation of heterogeneous bioinformatics databases.ResultsWe introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research.ConclusionBioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Dataset Information

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Publications

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets