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Overview

The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

Key Features

Circleator...

Prerequisites

Getting Started

First, install Circleator. After installing Circleator and its prerequisites, running the program requires as little as:

  1. A GenBank flat file for a genome of interest.
  2. A Circleator configuration file.

Examples of both of these types of files can be found in the Circleator source distribution. For example, from the top level of the unpacked Circleator zip or tar file the following command will create a Circleator figure for CM000961.gbk, which contains the genome of Corynebacterium genitalium ATCC 33030:

   circleator --data=data/CM000961.gbk --config=conf/genes-percent-GCskew-1.cfg > fig1.svg

The resulting SVG file, fig1.svg can be viewed directly in many recent web browsers or image viewers. Or, if the Apache Batik package has been installed, it can be used to convert the image to PDF, PNG, or JPEG, using a wrapper script (rasterize-svg) from the Circleator distribution:

   rasterize-svg fig1.svg pdf
   rasterize-svg fig1.svg png
   rasterize-svg fig1.svg jpeg

Advanced Features

The Circleator configuration file format aims to make the common case fast and the uncommon case possible. In other words, new users should be able to quickly produce a standard visualization of their data, provided it is in a commonly-used format. Conversely, experienced users should be able to create intricately-customized figures by using the same configuration file syntax.

For new users:

For experienced users:

Copyright

Circleator is Copyright (C) 2010-2017, Jonathan Crabtree <jonathancrabtree@gmail.com>

Licensing

Circleator is free software and is distributed under the terms of the Artistic License 2.0. For details, see the full text of the license in the file LICENSE in the top-level of this distribution.

Files with different licenses or copyright holders:

conf/brewer.txt

Copyright (c) 2002 Cynthia Brewer, Mark Harrower, and The Pennsylvania State University. The color specifications in this file are covered by an Apache-Style license. Please see the license statement in the file for details. The file itself was prepared by Martin Krzywinski and downloaded from http://mkweb.bcgsc.ca/brewer/swatches/brewer.txt

Acknowledgments

This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org).

Citation

An Applications Note describing Circleator has been published in Bioinformatics:

Crabtree, J., Agrawal, S., Mahurkar, A., Myers, G.S., Rasko, D.A., White, O. (2014) Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG. Bioinformatics, 10.1093/bioinformatics/btu505.