📄️ Building a pangraph
This short tutorial will walk you through the process of generating a pangraph from a set of bacterial genomes. We will also cover how to export the generated pangraph file into other formats.
📄️ The structure of Pangraph output file
In this second part of the tutorial we will explore in more detail the content of the json output file produced by the build command.
📄️ Exporting sequences
Pangraph's export command also allows the export of nucleotide sequences from the graph. We will cover:
📄️ Projecting the graph on a subset of strains.
In this next part of the tutorial we show how to use the simplify command. This command is used when one is interested in the relationship between a subset of the genomes that make up the pangraph. It can quickly create, starting from the full pangraph, a smaller pangenome graph relative to the selected subset of strains.
📄️ Example application: plasmid rearrangements
These next two tutorials cover other possible applications of pangraph and processing the downstream output.
📄️ Example application: antibiotic resistance gene neighbourhoods
Regions around antibiotic resistance genes are often structurally diverse, due to the high numbers of rearrangements e.g. those arising from repeated insertions of different insertion sequences (ISs). In this tutorial we'll use pangraph to explore a dataset of isolates which all contain a beta-lactamase gene: KPC-2 or KPC-3 (1 SNP difference). Rather than look at the whole genomes, we will explore just the immediate neighbourhood of the KPC gene.