Pantograph is an interactive browser for pangenome graphs. Pangenome graphs store the alignments between multiple individual DNA sequences in a compressed form. The Pantograph visualization scheme transforms the graph structure into a multiple sequence alignment-like binary matrix form.

Pantograph Views

Pantograph offers these main pages highlighting different data:

• Genome View: Start page providing an overview of all chromosomes
• Graph View: View of chromosome-specific pangenome graphs
• Pipeline Page: View pipeline results and states

Getting Started

The start page of Pantograph lets the user navigate to the Graph View of a specific chromosome-specific pangenome graph (by clicking on the chromosome) or to the concrete pangenome location of a specific gene (by selecting a gene in the gene selection menu in the left sidebar).

The Graph View browses the chromosome-specific pangenome graphs. Graph tracks with gene annotations, variant tracks and QTL tracks together with any metadata information can be explored all together in combined views.

User Interaction in Pantograph

Read about the main ways of navigating the data hub and an overview about the typical user interaction features.

Explore Genotype-Phenotype Associations

Pantograph offers several ways in visually exploring marker-trait associations:

• Sort tracks by metadata categories (right-click menu or click on arrows on top of metadata columns)
• Plot metadata distributions for individual columns (right-click menu: "Plot by metadata")
• Cluster custom regions by sequence and generate an interactive phylogenetic tree

Update Data

Most data can be extended or updated by admin users of Pantograph:

• Upload metadata
• Upload variation tracks
• Upload expression data

Getting Help

Please send bug reports or any questions how to use Pantograph to:

pantograph.support@computomics.com