Circleator - Documentation

Installation

Please see the Installation Guide for detailed download and installation instructions.

Running Circleator

The current release of Circleator only provides a command-line interface, documented below:

• Circleator command line usage

A prototype ExtJS web interface has been developed and split off into a separate project/repository (“Ringmaster”).

Tutorials

Detailed tutorials for common data types and figure formats:

• GenBank Flat File Visualization - display the sequence and/or annotation from a GenBank flat file
• Coverage Plots Using BAM Files - view coverage plots of RNA-Seq and other types of BAM-encoded alignment data.
• Gene Conservation Visualization - visualize patterns of gene conservation in two or more closely-related strains or serovars.
• Displaying SNPs and indels - show SNPs and/or indels in one or more microbial strains relative to a reference genome and gene set.

Work is still ongoing for the following tutorial(s). If you’re interested in more information on displaying these datatypes, get in touch with us via e-mail or the Circleator Google group:

• Graphs and heat maps - ways to display quantitative data using graphs and heat maps.

Reference Material

• Circleator README file
• Configuration file format
• Predefined track types
• Gallery of sample figures

Additional Resources

• The Circleator source code is available from GitHub.
• Questions/comments may be directed to the Circleator Google group.
• Bugs may also be reported via the issue tracker on GitHub.