Project: GTDBTk (GitHub Link)

GTDBTk-master
- gtdbtk
  - misc.py
  - classify.py
  - markers.py
  - exceptions.py
  - biolib_lite
    - custom_help_formatter.py
    - exceptions.py
    - newick.py
    - prodigal_biolib.py
    - seq_io.py
    - taxonomy.py
    - execute.py
    - logger.py
    - common.py
    - __init__.py
    - parallel.py
  - relative_distance.py
  - reroot_tree.py
  - tools.py
  - config
    - config_template.py
    - config.py
    - output.py
    - __init__.py
  - external
    - tigrfam_search.py
    - pypfam
      - Scan
        PfamScan.py
        __init__.py
      - HMM
        HMMResults.py
        HMMMatch.py
        __init__.py
        HMMSequence.py
        HMMResultsIO.py
        HMMUnit.py
      - __init__.py
    - pfam_search.py
    - mash.py
    - fastani.py
    - fasttree.py
    - __init__.py
    - hmm_aligner.py
    - pplacer.py
    - prodigal.py
  - trim_msa.py
  - decorate.py
  - __main__.py
  - VERSION
  - io
    - marker
      - tophit.py
      - copy_number.py
      - __init__.py
    - prodigal
      - tln_table.py
      - tln_table_summary.py
      - __init__.py
    - __init__.py
  - __init__.py
  - main.py
  - tests
    - data
      - genomes
  - infer_ranks.py
  - ani_rep.py
- LICENSE
- setup.py
- README.md
- tests
  - test_gtdbtk
    - test_trim_msa.py
    - test_markers.py
    - test_main.py
    - test_external
      - test_fastani.py
      - __init__.py
    - test_biolib_lite
      - test_seq_io.py
      - test_newick.py
      - test_common.py
      - __init__.py
    - test_io
      - test_prodigal
        test_tln_table_summary.py
        __init__.py
      - __init__.py
      - test_marker
        test_copy_number.py
        test_tophit.py
        __init__.py
    - __init__.py
    - test_tools.py
  - test_classify.py
  - data
    - pplacer_dir_reference
      - gtdbtk.ar122.classify.tree
    - identify_dir_reference
      - gtdbtk.bac120.markers_summary.tsv
      - identify
        gtdbtk.bac120.markers_summary.tsv
        intermediate_results
        marker_genes
        genome_1
        genome_1_pfam.tsv
        genome_1_pfam.tsv.sha256
        genome_1_tigrfam.tsv.sha256
        genome_1_tigrfam.tsv
        genome_1_pfam_tophit.tsv.sha256
        prodigal_translation_table.tsv
        genome_1_tigrfam_tophit.tsv
        genome_1_pfam_tophit.tsv
        genome_1_tigrfam_tophit.tsv.sha256
        genome_2
        genome_2_tigrfam.tsv.sha256
        genome_2_tigrfam.tsv
        genome_2_pfam_tophit.tsv
        genome_2_tigrfam_tophit.tsv
        genome_2_pfam_tophit.tsv.sha256
        genome_2_pfam.tsv.sha256
        genome_2_pfam.tsv
        prodigal_translation_table.tsv
        genome_2_tigrfam_tophit.tsv.sha256
        genome_3
        genome_3_pfam.tsv.sha256
        genome_3_tigrfam.tsv
        genome_3_pfam.tsv
        genome_3_pfam_tophit.tsv
        genome_3_pfam_tophit.tsv.sha256
        genome_3_tigrfam_tophit.tsv
        genome_3_tigrfam.tsv.sha256
        prodigal_translation_table.tsv
        genome_3_tigrfam_tophit.tsv.sha256
        gtdbtk.translation_table_summary.tsv
        gtdbtk.ar122.markers_summary.tsv
      - gtdbtk.translation_table_summary.tsv
      - gtdbtk.ar122.markers_summary.tsv
    - genomes_gz
    - align_dir_reference
      - align
        gtdbtk.ar122.user_msa.fasta
        intermediate_results
        gtdbtk.bac120.marker_info.tsv
        gtdbtk.ar122.marker_info.tsv
        gtdbtk.ar122.filtered.tsv
      - identify
        gtdbtk.bac120.markers_summary.tsv
        gtdbtk.translation_table_summary.tsv
        gtdbtk.ar122.markers_summary.tsv
  - test_cli.py
  - common.py
  - __init__.py
- scripts
  - trim_msa_based_on_mask.py
  - remove_user_genomes.py
  - verify_official_package.py
  - rename_UBAs
    - prepare_gtdbtk_package.py
  - gtdb_to_ncbi_majority_vote.py
- Dockerfile
- .gitignore
- docs
  - faq.md
  - running
    - docker.md
    - index.md
    - bioconda.md
    - kbase.md
    - pip.md
  - _config.yml
  - references.md
  - files
    - ani_closest.tsv.md
    - fasttree.log.md
    - mash_distances.msh.md
    - prodigal_translation_table.tsv.md
    - user_query_sketch.msh.md
    - gtdbtk_ref_sketch.msh.md
    - summary.tsv.md
    - test_execution.log.md
    - red_dictionary.tsv.md
    - protein.faa.md
    - index.md
    - classify.tree.md
    - unrooted.tree.md
    - gtdbtk.warnings.log.md
    - pfam_tophit.tsv.md
    - ani_summary.tsv.md
    - pplacer.domain.out.md
    - msa.fasta.md
    - tigrfam.out.md
    - user_msa.fasta.md
    - filtered.tsv.md
    - markers_summary.tsv.md
    - gtdbtk.log.md
    - translation_table_summary.tsv.md
    - tigrfam.tsv.md
    - tigrfam_tophit.tsv.md
    - pplacer.domain.json.md
    - tree.log.md
    - protein.fna.md
    - pfam.tsv.md
    - marker_info.tsv.md
    - protein.gff.md
    - classification_pplacer.tsv.md
  - commands
    - classify_wf.md
    - classify.md
    - test.md
    - align.md
    - export_msa.md
    - ani_rep.md
    - root.md
    - index.md
    - check_install.md
    - identify.md
    - infer.md
    - de_novo_wf.md
    - decorate.md
    - trim_msa.md
  - announcements.md
  - index.md
  - README.md
- MANIFEST.in

GTDB-Tk

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.

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.