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A Customizable Protocol for String Assembly gRNA Cloning (STAgR)

A Customizable Protocol for String Assembly gRNA Cloning (STAgR)

Published on: December 26, 2018

agtools: a software framework to manipulate assembly graphs.

Vijini Mallawaarachchi¹, George Bouras^2,3, Ryan R Wick^4,5

¹Flinders Accelerator for Microbiome Exploration, Flinders University, Bedford Park, SA 5042, Australia.

Bioinformatics Advances

|May 25, 2026

Summary

This summary is machine-generated.

agtools is an open-source Python framework for manipulating assembly graphs from genome and metagenome assemblers. It offers command-line and package interfaces for streamlined graph analysis and integration into bioinformatics workflows.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Assembly graphs are crucial data structures for genome and metagenome assemblers, representing sequence overlaps.
These graphs are increasingly vital for downstream applications like metagenomic binning, plasmid detection, and haplotype phasing.
A comprehensive tool for manipulating diverse assembly graph formats is needed.

Purpose of the Study:

To present agtools, an open-source Python framework for manipulating assembly graphs.
To provide programmatic access for parsing, converting, filtering, and analyzing assembly graphs.
To facilitate streamlined, integrated assembly-graph-based bioinformatics analyses.

Main Methods:

Developed an open-source Python framework named agtools.
Implemented a command-line interface for tasks like format conversion, filtering, and component extraction.
Exposed a Python package interface for loading, querying, and analyzing assembly graphs.

Main Results:

agtools supports assembly graphs from popular genome and metagenome assemblers.
The framework enables efficient manipulation and analysis of assembly graph data.
Provides streamlined integration into existing bioinformatics software and workflows.

Conclusions:

agtools offers a versatile solution for assembly graph manipulation.
The tool enhances downstream analyses in genomics and metagenomics.
agtools is readily available via GitHub, Bioconda, and PyPI.