Package: gtdbtk
GTDB-TkGTDB-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 theGNU General Public License (Version 3).Notifications about GTDB-Tk releases will be available through theGTDB Twitteraccount and theGTDB Announcements Forum.Please post questions and issues related to GTDB-Tk on the Issues section of the GitHub repository. Questions
related to theGTDBcan be posted on theGTDB Forumor sent to theGTDB team.🚀 Getting startedBe sure to check thehardware requirements, then choose your preferred method:BiocondaDockerpip📖 DocumentationDocumentation for GTDB-Tk can be foundhere.✨ New FeaturesGTDB-Tk v2.3.0+ includes the following new features:New functionalityconvert_to_speciesfunction to convert GTDB genome IDs to GTDB species names📈 PerformanceUsing ANI screen "can" reduce computation by >50%, although it depends on the set of input genomes. A set of input genomes consisting primarily of new species will not benefit from ANI screen as much as a set of genomes that are largely assigned to GTDB species clusters. In the latter case, the ANI screen will reduce the number of genomes that need to be classified by pplacer which reduces computation time substantially (between 25% and 60% in our testing).📚 ReferencesGTDB-Tk is described in:Chaumeil PA, et al. 2022.GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database.Bioinformatics, btac672.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. (2021).GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.Nucleic Acids Research,50: D785–D794.Rinke, C, et al. (2021).A standardized archaeal taxonomy for the Genome Taxonomy Database.Nature Microbiology,6: 946–959.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 Biol17, 132. doi: 10.1186/s13059-016-0997-x.© CopyrightCopyright 2017 Pierre-Alain Chaumeil. See LICENSE for further details.