KEGGaNOG

Motivation

eggNOG-mapper 🤝 KEGG-Decoder

• eggNOG-mapper is a comprehensive tool for fast functional annotation of novel sequences. Yet it does not provide any visualization functions.
• KEGG-Decoder is a perfect tool for visualizing KEGG Pathways. But it only takes KEGG-Koala outputs as an input (including blastKOALA, ghostKOALA, KOFAMSCAN).
• KEGG-Koala is a web-tool which can work for more than 24 hours. eggNOG-mapper can be installed locally on your PC / server and work faster.
• This tool KEGGaNOG makes eggNOG-mapper meet KEGG-Decoder! It parses eggNOG-mapper output, make it fit for the input to KEGG-Decoder and then visualize KEGG Pathways as the heatmap!
• Pro-tip: eggNOG-mapper and KEGGaNOG could be wrapped into 🐍 Snakemake pipeline making metabolic profiling a "one-click" process!

Installation

```bash

Linux / WSL / macOS

conda create -n kegganog pip -y conda activate kegganog pip install kegganog ```

Usage Guide

``` usage: KEGGaNOG [-h] [-M] -i INPUT -o OUTPUT [-overwrite] [-dpi DPI] [-c COLOR] [-n NAME] [-g] [-V]

KEGGaNOG: Link eggNOG-mapper and KEGG-Decoder for pathway visualization.

options: -h, --help show this help message and exit -M, --multi “Multi” mode allows to run KEGGaNOG on multiple eggNOG-mapper annotation files (a text file with file location paths must be passed to the input) -i INPUT, --input INPUT Path to eggNOG-mapper annotation file -o OUTPUT, --output OUTPUT Output folder to save results -overwrite, --overwrite Overwrite the output directory if it already exists -dpi DPI, --dpi DPI DPI for the output image (default: 300) -c COLOR, --color COLOR, --colour COLOR Cmap for seaborn heatmap. Recommended options: Greys, Purples, Blues, Greens, Oranges, Reds (default: Blues) -n NAME, --name NAME Sample name for labeling (default: SAMPLE) (not active in --multi mode) -g, --group Group the heatmap based on predefined categories -V, --version show program's version number and exit ```

🔗 Please visit KEGGaNOG wiki page

Output examples gallery

Default visualization

|Single mode|Multi mode| |-----------|----------| |||

These figures are generated using functional groupping mode (-g/--group) and Greens colormap

User APIs visualization

|Barplot|Boxplot|Radarplot|Correlation Network| |-------|-------|---------|-------------------| |||||

|Stacked Barplot|Streamgraph|Stacked Barplot + Streamgraph| |-------|-------|-------| ||||

Advantages

1. Seemless Access to KEGG Annotations: Provides KEGG Ortholog (KO) annotations without requiring a KEGG license.
2. High-Throughput Capability: Optimized for rapid KO assignment in large-scale datasets, ideal for metagenomics and genomics projects.
3. Broad Functional Coverage: Leverages the extensive eggNOG database to annotate genes across a wide range of taxa.

Limitation

1. Indirect KO Mapping: eggNOG-mapper doesn’t directly use the KEGG database, its KO term assignments are inferred through orthologous groups (eggNOG entries). This can sometimes result in less precise annotations.

Tool name background

KEGGaNOG stands for “KEGG out of NOG”, highlighting its purpose: extracting KEGG Ortholog annotations from eggNOG’s Non-supervised Orthologous Groups.

Contributing

Contributions are welcome! If you have any ideas, bug fixes, or enhancements, feel free to open an issue or submit a pull request.

Contact

For any inquiries or support, feel free to contact me via email

Happy functional annotation! 💻🧬

Acknowledgements

For now KEGGaNOG uses KEGG-Decoder as a main dependecy. I greatly thank KEGG-Decoder's developers.