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
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. GitHub

Third-party GTDB Databases

Databases Description Authors Link
HUMANn 2, Kraken 2, Bracken 2 HUMANn 2, Kraken 2 and Bracken 2 databases (see bioRxiv preprint). Jacobo de la Cuesta-Zuluaga, Ruth Ley, Nicholas Youngblut GitHub
Centrifuge, Kraken Centrfuge, Kraken 1, and Kraken 2 databases (see bioRxiv preprint). Guillaume Méric, Ryan Wick and colleagues Figshare
Kraken Kraken database. Henk den Bakker and Lee Katz. GitHub
DADA 2 DADA2 16S rRNA database. Ali Alishum and colleagues. Zenodo

Third-party Scripts

Script Description Authors Link
tax_from_gtdb.py Generate NCBI-style taxonomy files from GTDB taxonomy files. Ryan Wick GitHub
genome_updater Bash script to download and update snapshots of the NCBI genomes (refseq/genbank). Vitor C. Piro GitHub
gtdb_to_taxdump Convert GTDB taxonomy to NCBI taxdump format. Nick Youngblut GitHub