Greengenes Dataset (modified for deeptaxa)

This dataset contains 16S rRNA gene sequences with hierarchical taxonomic annotations, designed for training and evaluating models like DeepTaxa. It is a processed version of the Greengenes database, widely used in microbiome research.

Dataset Details

• Files:
  • gg_2024_09_training.fna.gz: Training sequences (FASTA)
  • gg_2024_09_training.tsv.gz: Training labels (TSV)
  • gg_2024_09_testing.fna.gz: Testing sequences (FASTA)
  • gg_2024_09_testing.tsv.gz: Testing labels (TSV)
  • gg_2024_09_training_ids.txt: Training sequence IDs
  • gg_2024_09_testing_ids.txt: Testing sequence IDs
• Format: FASTA (sequences), TSV (labels with 7 taxonomic levels)
• Source: Derived from Greengenes (DeSantis et al., 2006)

Usage

Use with DeepTaxa:

deeptaxa train --fasta-file gg_2024_09_training.fna.gz --taxonomy-file gg_2024_09_training.tsv.gz

Models

This dataset is compatible with the DeepTaxa.

License

This dataset is a modified version of the Greengenes2 dataset, used for training and testing DeepTaxa. It is distributed under the terms of the Modified BSD License, as required by the original Greengenes2 license.

Original Greengenes2 License

Copyright (c) 2022-, Greengenes2 [email protected]

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Greengenes2 nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BIOM FORMAT DEVELOPMENT TEAM BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Modifications

This modified version (gg_2024_09) was created by the Systems Genomics Lab for use with DeepTaxa. The modifications include splitting the dataset into training and testing sets and adding ID files.

Copyright (c) 2025, Systems Genomics Lab

Distributed under the same Modified BSD License terms as the original Greengenes2 dataset.

Citation

For the dataset:

@article{DeSantis2006,
  author = {DeSantis, T. Z. and Hugenholtz, P. and Larsen, N. and Rojas, M. and Brodie, E. L. and Keller, K. and Huber, T. and Dalevi, D. and Hu, P. and Andersen, G. L.},
  title = {Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB},
  journal = {Applied and Environmental Microbiology},
  year = {2006},
  doi = {10.1128/AEM.03006-05}
}

For DeepTaxa: See GitHub.

Contact

Report issues on GitHub.