agtools: A Software Framework to Manipulate Assembly Graphs

agtools is a Python framework for manipulating assembly graphs for downstream metagenomic applications, with a focus on the Graphical Fragment Assembly (GFA) format. It offers a command-line interface for tasks such as graph format conversion, segment filtering, and component extraction. Supported formats include GFA, FASTG, ASQG and GraphViz DOT. In addition, it provides a Python package interface that exposes assembler-specific functionality for advanced analysis and integration based on the GFA format.

Quick install

Install using pip:

pip install agtools

Install from the Bioconda distribution using conda or mamba:

mamba install -c bioconda agtools

Further details are available in the Installation Guide.

Documentation

Tutorials

• CLI examples
• API tutorial
• Assembler-specific examples
• More detailed examples
• Example applications

References

• CLI reference
• API reference
• File formats
• Source code

Support

• Changelog
• FAQ

Citation

agtools is currently under review. In the meantime, if you use agtools in your work, please cite the preprint as follows.

Vijini Mallawaarachchi, George Bouras, Ryan R. Wick, Susanna R. Grigson, Bhavya Papudeshi, Robert A. Edwards; agtools: a software framework to manipulate assembly graphs; bioRxiv 2025.09.14.676178; doi: https://doi.org/10.1101/2025.09.14.676178