GTDB-Tk

GTDB-Tk v2.0.1 was released on April xx, 2022 along with new reference data for GTDB R07-RS207. Upgrading is recommended.
Please note v2.0.1+ is not compatible with GTDB R06-RS202.

GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

Notifications about GTDB-Tk releases will be available through the GTDB Twitter account (https://twitter.com/ace_gtdb).

Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions related to the GTDB should be sent to the GTDB team.

New Features

GTDB-Tk v2.0.1 includes the following new features:

• Classification is done by default using a divide-and-conquer strategy to systematically reduce the size of the reference tree and associated memory requirements. When running with R07-RS207, GTDB-Tk requires 320GB of RAM for the pplacer step with the full bacterial tree. The divide-and-conquer approach reduces this requirement to around 20GB of RAM.
  This is now the default approach in GTDB-Tk.
  To use the full bacterial reference tree in the classification step, use the -f,--full-tree flag.
• Archaeal classification now uses a refined set of 53 archaeal-specific marker genes based on a recent published analysis of archaeal markers (similar to GTDB R07-RS207).
• To reduce the size of the output directory,
  • all intermediate_results folders ( in identify,align,classify,infer) are now removed after the end of the classify_wf and de_novo_wf pipelines. To keep intermediates files use the flag --keep-intermediates.
  • all msa output from the align step are now automatically archived (.gz).
• The summary files and failed genomes files are now the only files linked in the root directory of classify_wf.

Documentation

https://ecogenomics.github.io/GTDBTk/

References

GTDB-Tk is described in:

• Chaumeil PA, et al. 2019. GTDB-Tk: A toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, btz848.

The Genome Taxonomy Database (GTDB) is described in:

• Parks, D.H., et al. 2020. A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology, https://doi.org/10.1038/s41587-020-0501-8.

• Parks DH, et al. 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, http://dx.doi.org/10.1038/nbt.4229.

We strongly encourage you to cite the following 3rd party dependencies:

• Matsen FA, et al. 2010. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11:538.
• Jain C, et al. 2019. High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries. Nat. Communications, doi: 10.1038/s41467-018-07641-9.
• Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11:119. doi: 10.1186/1471-2105-11-119.
• Price MN, et al. 2010. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One, 5, e9490.
• Eddy SR. 2011. Accelerated profile HMM searches. PLOS Comp. Biol., 7:e1002195.
• Ondov BD, et al. 2016. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132. doi: doi: 10.1186/s13059-016-0997-x.

Copyright

Copyright 2017 Pierre-Alain Chaumeil. See LICENSE for further details.