GView

gview_general_1.pngGView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts. For examples of some of the images GView can produce, see the Image Gallery.

GView is a re-write of CGView, a circular genome viewer written by Paul Stothard. The goal of GView is to provide greater user interaction, and more flexibility in how the genome map is rendered. To aid with easily configuring the display of a genome, a style editor has been included to provide an intuitive, user-friendly graphical user interface for customizing genome maps. Styling attributes such as colours or fonts for the various map elements can be adjusted in real time. Customized styles can be saved for later use or for application to other genome maps using GView's custom file format.

In addition to the GView software package, a web server, GView Server, has been developed for comparative genome analysis tasks. GView Server helps guide users along the way of uploading and preparing data to generate specialized maps in GView such as a BLAST Atlas, Pangenomes, Core Genomes, and many more. Please see the documentation on the GView Server site for more information.

It is possible for developers to integrate GView in a Java application, allowing developers to create and render genomic maps within external applications. Users interacting with GView from within another application will have the same user interaction abilities as the GView stand-alone application. Visit GView API for more information.

To test GView, please try out the GView Java Web Start version. For more complex tasks, a standalone version of GView can be downloaded.

Latest Release Features:
  • Intuitive pan-and-zoom interface
  • Linear or Circular genome backbone layouts
  • Static images exported in png, jpg or svg format
  • Style editor to modify the appearance
  • Backwards compatible with CGView XML or Tab delimited formats
  • API for integrating GView with Java applications

Citing GView

Petkau A, Stuart-Edwards M, Stothard P, and Van Domselaar G. Interactive microbial genome visualization with GView. Bioinformatics 2010 26: 3125-3126.
 
Contact: Aaron Petkau, Eric Marinier, Matthew Stuart-Edwards at gview@phac-aspc.gc.ca