GTAXOPROP (Genbinesia Taxonomy Propagator)

GTAXOPROP is a utility to generate input files for taxonomy propagation and assignment in QIIME/QIIME2 from the NCBI database. It converts NCBI accession numbers to QIIME/QIIME2-compatible taxonomy files with API fallback.

⚠️ Derivative Work Notice

GTAXOPROP is a derivative work based on entrez_qiime v2.0 by Christopher C. M. Baker. This version includes substantial modifications and enhancements while maintaining GPL v3 compliance.

Original work: Baker, C.C.M. (2016). entrez_qiime. v2.0. https://github.com/bakerccm/entrez_qiime

Major Enhancements from Original

• ✅ Complete Python 3 migration
• ✅ cogent3 integration (replaced PyCogent)
• ✅ Better NCBI Entrez communication using Biopython
• ✅ Advanced caching with resume capability
• ✅ Batch API processing with rate limiting
• ✅ Improved error handling and logging
• ✅ Enhanced file encoding detection
• ✅ Better taxonomy rank handling

Authors

• Maulana Malik Nashrulloh (Division of Biomics Research, Department of Sciences, Generasi Biologi Indonesia Foundation)
• Sonia Az Zahra Defi (Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University)
• Brian Rahardi (Department of Bioinformatics, Faculty of Mathematics and Natural Sciences, Brawijaya University)
• Muhammad Badrut Tamam (Division of Biomics Research, Department of Sciences, Generasi Biologi Indonesia Foundation & Biology Program, Faculty of Science, Technology, and Education, Muhammadiyah University of Lamongan)
• Riki Ruhimat (Research Center for Applied Microbiology, Research Organization for Life Sciences, National Research and Innovation Agency)
• Hessy Novita (Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency)

Quick Start

Dependencies

Make sure that your system have Python >=3.10 installed and these packages/libraries installed:

• tinydb==4.8.2
• pbr>=6.1.1
• stevedore>=5.5.0
• cogent3>=2025.9.8a2
• biopython>=1.85

Installation

Currently we only support installation thru pip command only.

pip install gtaxoprop

Usage

To use this program, you must have NCBI taxdump and accession2taxid data

• taxdump.tar.gz (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz). This tarball contains files that constitute the full NCBI taxonomy database, primarily used for local installations and bioinformatics tools that require taxonomic information
• nucl_gb.accession2taxid.gz (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz). This file store TaxID mapping for live nucleotide sequence records of type WGS or TSA.
• nucl_wgs.accession2taxid.gz (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz). This file store TaxID mapping for live nucleotide sequence records that are not WGS or TSA.

Unpacked content of nucl_gb.accession2taxid.gz and nucl_wgs.accession2taxid.gz respectively is very huge! (Spending 10 GB+ and 40 GB+ space respectively, manage your disk space accordingly!). Alternatively, you may choose only one, nucl_gb.accession2taxid.gz or nucl_wgs.accession2taxid.gz one, but this may will not cover entirety of your data.

Assumed that you have enough free space of 100-150 GB+ at your ~ (/home/username/), run this command one-by-one to set up your data:

cd ~
mkdir ~/path/to/your/NCBI/taxdump
cd ~/path/to/your/NCBI/taxdump
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -zxvf taxdump.tar.gz
mkdir ~/path/to/your/NCBI/accession2taxid
cd ~/path/to/your/NCBI/accession2taxid
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
gunzip nucl_gb.accession2taxid.gz
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz
gunzip nucl_wgs.accession2taxid.gz
cp nucl_gb.accession2taxid nucl_merged.accession2taxid
tail -n+2 nucl_wgs.accession2taxid >> nucl_merged.accession2taxid
rm nucl_gb.accession2taxid nucl_wgs.accession2taxid

For propagating taxonomy of Archaea, Bacteria, and Eukaryota:

gtaxoprop -i ~/path/to/your/your_sequences.fasta \
          -o ~/path/to/your/your_taxdumps.txt \
          -g ~/path/to/your/your_execution.log \
          -n ~/path/to/your/NCBI/taxdump/ \
          -a ~/path/to/your/NCBI/accession2taxid/nucl_merged.accession2taxid \
          -r domain,kingdom,phylum,class,order,family,genus,species \
          -d \
          --email your_mail@email.xxx

For propagating taxonomy of Virus:

gtaxoprop -i ~/path/to/your/your_sequences.fasta \
          -o ~/path/to/your/your_taxdumps.txt \
          -g ~/path/to/your/your_execution.log \
          -n ~/path/to/your/NCBI/taxdump/ \
          -a ~/path/to/your/NCBI/accession2taxid/nucl_merged.accession2taxid \
          -r realm,kingdom,phylum,class,order,family,genus,species \
          -d \
          --email your_mail@email.xxx

Help

To access the help, use:

gtaxoprop -h

Acknowledgments

• This program is based on entrez_qiime Version 2.0 by Chris Baker (https://github.com/bakerccm/entrez_qiime)
• Part of this program was presented at 4th International Conference on Biological Sciences (ICoBioS 2025) (https://www.icobios.org/)
• This program was made as part of research mini-project "In silico metagenomic assessment of aCPSF1 phylogenetic marker for the identification and classification of archaea using publicly available Metagenomic Whole-genome Shotgun Sequencing data" funded internally by Generasi Biologi Indonesia Foundation.

Citation

A dedicated publication for this program is not yet available. For citation purposes, please refer to the following technical report:

Nashrulloh, M.M., Defi, S.A.Z., Rahardi, B., Tamam, Mh. B., Ruhimat, R., & Novita, H. (2025). GTAXOPROP: A utility to generate input files for taxonomy propagation and assignment in QIIME/QIIME2 from the NCBI database (Technical Report No. GBR-TR-BIOMIKA-01/Genbinesia/IX/2025). Generasi Biologi Indonesia Foundation. Gresik, Indonesia.

If you wish to cite this repository, you may use the following APA-style reference entry:

Nashrulloh, M.M., Defi, S.A.Z., Rahardi, B., Tamam, Mh. B., Ruhimat, R., & Novita, H. (2025). GTAXOPROP: A utility to generate input files for taxonomy propagation and assignment in QIIME/QIIME2 from the NCBI database (Version 1.0.post3) [Computer software]. https://gitlab.com/biomikalab/GTAXOPROP

License

This project is licensed under the GNU General Public License v3.0 - See the LICENSE file for details.