GTDB-Tk

GTDB-Tk classifies bacterial and archaeal genomes against the Genome Taxonomy Database (GTDB) to provide objective taxonomic assignments for isolate, single-cell, and metagenome-assembled genomes (MAGs).

Key Features:

• GTDB-based taxonomic assignment: Assigns taxonomy using the Genome Taxonomy Database (GTDB).
• Genome type support: Handles metagenome-assembled genomes (MAGs), isolate genomes, and single-cell genomes.
• Scalability and parallel processing: Provides computational efficiency and parallel processing to classify thousands of draft genomes and large datasets simultaneously.
• Validation on diverse MAGs: Accuracy validated on a phylogenetically diverse set of 10,156 bacterial and archaeal MAGs.
• Design for high-throughput genomics: Suited to datasets produced by recent genomic technologies that assemble hundreds to thousands of MAGs.

Scientific Applications:

• Environmental metagenomics: Taxonomic classification of MAGs recovered from complex environmental samples.
• Isolate and single-cell genomics: Taxonomic placement of cultured isolates and single-cell amplified genomes.
• Large-scale genomic surveys: Enabling taxonomic analysis across studies comprising hundreds to thousands of genomes.

Methodology:

Performs taxonomic classification against the Genome Taxonomy Database (GTDB) and is implemented in Python.