TaxonReportViewer (TRV)

About

Features

Downloads

License

Authors

Citation

About

TaxonReportViewer (TRV) is an open-source, cross-platform graphical user interface (GUI) software designed to simplify and accelerate the exploration, comparison, and visualization of Kraken2 taxonomic classification outputs. Shotgun metagenomics enables comprehensive analysis of microbial communities by classifying sequencing reads directly from environmental samples, yet interpreting the resulting taxonomic classification reports—especially those generated by tools like Kraken2—remains a challenge due to their hierarchical, text-based format. Existing visualization tools such as Krona and Pavian either rely on web infrastructure or provide limited interactivity and flexibility for comparative analysis.

TRV addresses this critical gap by providing an intuitive and efficient bridge between raw metagenomic classification data and its subsequent biological interpretation. Implemented in Python 3, TRV includes a robust parser capable of accurately reconstructing taxonomic hierarchies even from inconsistently formatted reports. The tool offers dynamic search and filtering of taxa, exportable abundance matrices, one-click generation of comparative bar charts and heatmaps, and direct links to the NCBI Taxonomy database. It supports analysis of multiple samples in parallel, allowing users to identify taxonomic patterns across conditions without requiring programming skills. TRV operates efficiently on standard consumer hardware and requires no installation beyond Python, ensuring accessibility for researchers in diverse computational environments. It functions identically on Windows, Linux and MacOS systems.

Features

TRV empowers researchers to derive meaningful insights from complex metagenomic datasets with ease, without the need for advanced command-line scripting skills. Key features include:

Robust Parsing:

Accurately reconstructs taxonomic hierarchies even from inconsistently formatted Kraken2 reports , by analyzing line indentation and taxonomic rank order.

Dynamic Search & Filtering:

Allows users to search for any taxon name and display its entire taxonomic sub-tree, enabling isolation and inspection of specific lineages. Includes a filter to show only species-level results.

Interactive Data Exploration:

Data is displayed in a Treeview that preserves original taxonomic organization and uses color-coding for main ranks, enhancing readability and immediate visual interpretation.

Selection for Comparative Analysis:

Users can select multiple taxa of interest directly from the interface via checkboxes for subsequent comparative analyses across different samples. An option to select or deselect all visible taxa at once streamlines the workflow.

Extraction of Reports and Abundance Matrices:

Allows exportation of displayed data into tab-separated values (TSV) format. Generates single-sample or comparative abundance matrices of target taxa across multiple loaded samples. Output matrices are formatted to be directly compatible with other statistical analysis tools, such as R or STAMP.

Integrated Data Visualization:

Comparative Bar Plots:

Generates a grouped bar plot comparing the abundance (read count) of multiple selected taxa across the different loaded samples.

Abundance Heatmaps:

Visualizes abundance distributions , with options for single-sample (showing selected/most abundant taxa) , comparative across samples (based on user-selected reference taxa) , and "simplified" interactive versions with tooltips on mouseover.

NCBI Integration:

Each line in the results table is a hyperlink that, when clicked, opens the corresponding page of the TaxID in the NCBI Taxonomy Browser , allowing for rapid verification and retrieval of additional information about the taxon.

Multi-sample Compatibility:

Supports parallel analysis of multiple Kraken2 reports in separate tabs , facilitating cross-sample comparisons and pattern identification.

Performance:

The GUI is responsive even with large report files (e.g., >100,000 lines) , with searches completed in under one second on typical consumer-grade hardware (Intel Core i5, 8 GB RAM).

Downloads

Pre-compiled executables for Windows, macOS, and Linux are available for direct use. No Python installation is required for these versions.

Windows:

Download TaxonReportViewer-Windows.zip

macOS:

Download TaxonReportViewer-macOS.zip

Linux:

Download TaxonReportViewer-Linux.zip

Running Pre-compiled Executables

After downloading and extracting the .zip file for your operating system:

Windows:

Navigate to the extracted folder and double-click TaxonReportViewer.exe.

macOS:

Drag the TaxonReportViewer.app to your Applications folder. Double-click it to run. On first run, you might need to right-click -> "Open" to bypass Gatekeeper.

Linux:

Navigate to the extracted folder in a terminal and run ./TaxonReportViewer. Ensure execute permissions are set: chmod +x TaxonReportViewer.

Contributing

We welcome contributions to the TaxonReportViewer project! Please refer to CONTRIBUTING.md for guidelines on how to submit issues, propose features, and contribute code.

License

See the LICENSE file for details.

Authors

Emanuel Razzolini

Claudia Regina de Souza

Citation

If you use TaxonReportViewer in your research, please consider citing our work:

Razzolini, E. & Souza, C.R.. (2025) TaxonReportViewer: Parsing and Visualizing Taxonomic Hierarchies in Metagenomic Datasets. bioRxiv 2025.06.07.658440; doi: https://doi.org/10.1101/2025.06.07.658440