📄️ About PyPangraph
PyPanGraph is a Python package to facilitate exploration and analysis of PanGraph output JSON files.
📄️ Installation
PyPanGraph can be installed from PyPi using pip:
📄️ Loading and exploring a graph
We start the tutorial by loading a pangenome graph object and exploring its properties. For this tutorial we will use the plasmids.json file that you can find in pypangraph repository under tests/data/plasmids.json
📄️ A look at the pangenome
In this next section of the tutorial we use some of the features of PyPangraph to explore the blocks that make up the pangenome graph, and extract information on the pangenome of our dataset.
📄️ Exploring block alignments
In this next tutorial section we explore block alignments in more detail.
📄️ Paths and core genome synteny
In this tutorial we will learn how to visualize paths in a pangraph and to survey changes in core-genome synteny.
📄️ Comparing two genomes in a dotplot
Decomposing genomes in separate blocks provides a very good starting point for pairwise comparison between genomes. The pangenome graph can easily be used to draw a dotplot between two different paths, in which lines represent shared blocks.