Third-party tools
AnnoTreeAnnoTree is an interactive bacterial tree of life enabling the visualization of millions of precomputed functional annotations.Homepage
IDTAXAA novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors (see manuscript).Homepage
SingleMSingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. It is able to differentiate closely related species even if those species are from lineages new to science.Homepage
sourmashsourmash is a command-line tool and Python library for computing hash sketches from DNA sequences, comparing them to each other, and plotting the results. Prepared databases for GTDB are provided.Homepage
Third-party GTDB databases
HUMANn 2, Kraken 2, Bracken 2HUMANn 2, Kraken 2 and Bracken 2 databases (see manuscript).Jacobo de la Cuesta-Zuluaga, Ruth Ley, Nicholas YoungblutGitHub Repository
Centrifuge, KrakenCentrfuge, Kraken 1, and Kraken 2 databases (see bioRxiv preprint).Guillaume Méric, Ryan Wick and colleaguesMonash University
KrakenKraken database.Henk den Bakker and Lee Katz.GitHub Repository
DADA 2DADA2 16S rRNA database.Ali Alishum and colleagues.Zenodo
SBDISBDI Sativa curated 16S GTDB database.Daniel Lundin, Anders Andersson and colleagues.Figshare
KMCPAccurate metagenomic profiler.Wei ShenGitHub
Third-party scripts
tax_from_gtdb.pyGenerate NCBI-style taxonomy files from GTDB taxonomy files.Ryan WickGitHub Repository
genome_updaterBash script to download and update snapshots of the NCBI genomes (refseq/genbank).Vitor C. PiroGitHub Repository
gtdb_to_taxdumpConvert GTDB taxonomy to NCBI taxdump format.Nick YoungblutGitHub Repository