Tools
Third-party tools
| Software | Description | Link |
|---|---|---|
| AnnoTree | AnnoTree is an interactive bacterial tree of life enabling the visualization of millions of precomputed functional annotations. | Homepage |
| iTOL | Interactive Tree Of Life is an online tool for the display, annotation and management of phylogenetic and other trees. | Homepage GTDB trees |
| IDTAXA | A novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors (see manuscript). | Homepage |
| SingleM | SingleM 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 |
| sourmash | sourmash 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
| Database | Description | Authors | Link |
|---|---|---|---|
| HUMANn 2, Kraken 2, Bracken 2 | HUMANn 2, Kraken 2 and Bracken 2 databases (see manuscript). | Jacobo de la Cuesta-Zuluaga, Ruth Ley, Nicholas Youngblut | GitHub Repository |
| Centrifuge, Kraken | Centrfuge, Kraken 1, and Kraken 2 databases (see bioRxiv preprint). | Guillaume Méric, Ryan Wick and colleagues | Monash University |
| Kraken | Kraken database. | Henk den Bakker and Lee Katz. | GitHub Repository |
| DADA 2 | DADA2 16S rRNA database. | Ali Alishum and colleagues. | Zenodo |
| SBDI | SBDI Sativa curated 16S GTDB database. | Daniel Lundin, Anders Andersson and colleagues. | Figshare |
| KMCP | Accurate metagenomic profiler. | Wei Shen | GitHub |
Third-party scripts
| Script | Description | Author | Link |
|---|---|---|---|
| tax_from_gtdb.py | Generate NCBI-style taxonomy files from GTDB taxonomy files. | Ryan Wick | GitHub Repository |
| genome_updater | Bash script to download and update snapshots of the NCBI genomes (refseq/genbank). | Vitor C. Piro | GitHub Repository |
| gtdb_to_taxdump | Convert GTDB taxonomy to NCBI taxdump format. | Nick Youngblut | GitHub Repository |