GTDB-Tk 2.1.1

GTDBtk-2.1.1

GTDB-Tk v2.1.0 was released on May 11, 2022. Upgrading is recommended.

Please note v2.1.0+ is not compatible with GTDB-Tk package R207_v1. It is necessary to upgrade to GTDB-Tk package R207_v2.

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 and the GTDB Announcements Forum.

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

New Features

GTDB-Tk v2.1.0 includes the following new features:

• GTDB-TK now uses a divide-and-conquer approach where the bacterial reference tree is split into multiple class-level subtrees. This reduces the memory requirements of GTDB-Tk from 320 GB of RAM when using the full GTDB R07-RS207 reference tree to approximately 55 GB. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the --full-tree flag.
  This is the main change from v2.0.0. The split tree approach has been modified from order-level trees to class-level trees to resolve specific classification issues (See #383).
• Genomes that cannot be assigned to a domain (e.g. genomes with no bacterial or archaeal markers or genomes with no genes called by Prodigal) are now reported in the gtdbtk.bac120.summary.tsv as ‘Unclassified’
• Genomes filtered out during the alignment step are now reported in the gtdbtk.bac120.summary.tsv or gtdbtk.ar53.summary.tsv as ‘Unclassified Bacteria/Archaea’
• --write_single_copy_genes flag in now available in the classify_wf and de_novo_wf workflows.

Documentation

Documentation for GTDB-Tk can be found here.

Activating the conda environment

Check out a node with qrsh and run:

1
2

bash
source /local/cluster/gtdbtk/activate.sh

To run over SGE, add the source line above to your shell script prior to running your gtdbtk commands.

Location, version, and DB location

1
2
3
4
5
6

$ which gtdbtk
/local/cluster/gtdbtk/bin/gtdbtk
$ gtdbtk --version
gtdbtk: version 2.1.1 Copyright 2017 Pierre-Alain Chaumeil, Aaron Mussig and Donovan Parks
$ echo $GTDBTK_DATA_PATH
/nfs1/CGRB/databases/GTDB/current

help message

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

$ gtdbtk --help

              ...::: GTDB-Tk v2.1.1 :::...

  Workflows:
    classify_wf -> Classify genomes by placement in GTDB reference tree
                     (identify -> align -> classify)
    de_novo_wf  -> Infer de novo tree and decorate with GTDB taxonomy
                     (identify -> align -> infer -> root -> decorate)

  Methods:
    identify -> Identify marker genes in genome
    align    -> Create multiple sequence alignment
    classify -> Determine taxonomic classification of genomes
    infer    -> Infer tree from multiple sequence alignment
    root     -> Root tree using an outgroup
    decorate -> Decorate tree with GTDB taxonomy

  Tools:
    infer_ranks     -> Establish taxonomic ranks of internal nodes using RED
    ani_rep         -> Calculates ANI to GTDB representative genomes
    trim_msa        -> Trim an untrimmed MSA file based on a mask
    export_msa      -> Export the untrimmed archaeal or bacterial MSA file
    remove_labels   -> Remove labels (bootstrap values, node labels) from an Newick tree
    convert_to_itol -> Convert a GTDB-Tk Newick tree to an iTOL tree


  Testing:
    test          -> Validate the classify_wf pipeline with 3 archaeal genomes
    check_install -> Verify third party programs and GTDB reference package

  Use: gtdbtk <command> -h for command specific help

software ref: https://github.com/Ecogenomics/GTDBTk
research ref: https://doi.org/10.1101/2022.07.11.499641
research ref: https://doi.org/10.1093/bioinformatics/btz848