Pantograph Documentation

Appearance

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 represents the graph structure in a special multiple sequence alignment style.

Pantograph Main Views ​

  • Genome View: Overview of all chromosome graphs and QTL regions
  • Graph View: Browser of chromosome-specific pangenome graphs

Getting Started ​

After login, the user can select a Project. A Project is a pangenome dataset, i.e. a set of chromosome-specific pangenome graphs.

After project selection, the Genome View 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 (dropdown in Toolbar or click on arrows on top of metadata columns)
  • Sort tracks by genetic diversity (right-click on columns)
  • Plot metadata distributions for individual columns (right-click menu: "Plot by metadata")
  • Plot metadata distributions for haplotypes by clustering custom regions by sequence, generating an interactive dendrogram, and defining the haplotype groups: see instructions here.
  • Cluster custom regions by sequence and generate an interactive dendrogram

Collaboration ​

Pantograph provides simple and powerful ways to store and share pangenome views between users.

Update Data ​

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

Getting Help ​

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

pantograph.support@computomics.com