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Publications

We insist on maintaining the highest scientific rigour and integrity in everything we do. These publications provide insight into some of the discoveries and advances that are at the core of our work.

Evaluation of the Microba Community Profiler (MCP) for taxonomic profiling of metagenomic datasets from the human gut microbiome

A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links betweenmicrobial species and disease states.
Parks DH, Rigato F, Krause L, ... , Tyson GW, Wood DL

A complete domain-to-species taxonomy for Bacteria and Archaea

The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. 
Parks DH, Chuvochina M, Chaumeil PA, ... , Mussig AJ, Hugenholtz P

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

The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the 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
Chaumeil PA, Mussig AJ, ..., Hugenholtz P, Parks DH. doi: 10.1093/bioinformatics/btz848
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