CGView

CGView is a Java package for generating high quality, zoomable maps of circular genomes.

Sample maps created using CGView are available here.

CGView was written and is maintained by Paul Stothard stothard@ualberta.ca.

CGView citation

Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.

Use CGView online

Proksee uses a JavaScript version of CGView to create interactive, web-based maps.

Using the CGView Docker image

Pull the Docker image:

docker pull pstothard/cgview

Download a test file:

wget https://paulstothard.github.io/cgview/downloads/prokka_multicontig.gbk

Run the Docker image and use cgview_xml_builder.pl to create a CGView XML file:

docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview perl /usr/bin/cgview_xml_builder.pl -sequence prokka_multicontig.gbk -gc_content T -gc_skew T -size large-v2 -tick_density 0.05 -draw_divider_rings T -custom showBorder=false title="Example map" titleFontSize="200" -output map.xml

Run the Docker image and use cgview.jar to create a graphical map from the XML file:

docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview java -jar /usr/bin/cgview.jar -i map.xml -o map.png

The map.png file is written to the current directory on the host system (as is map.xml from the first command).

Here is the map generated by the above commands:

The following commands generate a similar map but with feature labels and zoomed in on a region of interest:

docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview perl /usr/bin/cgview_xml_builder.pl -sequence prokka_multicontig.gbk -gc_content T -gc_skew T -size large-v2 -tick_density 0.05 -draw_divider_rings T -custom showBorder=false title="Example map" titleFontSize=200 labelFontSize=60 -feature_labels T -output map_labels.xml
docker run --rm -v "$(pwd)":/dir -u "$(id -u)":"$(id -g)" -w /dir pstothard/cgview java -jar /usr/bin/cgview.jar -i map_labels.xml -f png -o map_zoomed.png -z 10 -c 6600000

Here is the map generated by the above commands:

The staggered divider lines show the boundaries of contigs--to use regular divider lines add -show_contigs F to the end of the cgview_xml_builder.pl command.

The cgview_xml_builder.pl program has many options for altering the contents of the map. For details on what key-value pairs can be supplied using the -custom option of cgview_xml_builder.pl see this page. The XML output from cgview_xml_builder.pl can also be manually edited prior to running cgview.jar to further adjust map appearance. The cgview.jar program has options for changing some aspects of the map and for specifying the format of the image that is produced.

To generate maps that include the results of comparisons with other genomes, use the CGView Comparison Tool (CCT).

CGView options

The command-line interface is described in detail in the CGView documentation. The following information can be obtained using java -jar cgview.jar --help:

CGView - drawing circular genome maps.

DISPLAY HELP AND EXIT:

  usage:

    java -jar cgview.jar --help

DISPLAY VERSION AND EXIT:

  usage:

    java -jar cgview.jar --version

CREATE A SINGLE MAP IMAGE:

  usage:

    java -jar cgview.jar -i <file> -o <file> [Options]

    required arguments:

      -i  Input file in CGView XML or TAB format.
      -o  Output file to create.

    optional arguments (when used these override corresponding values specified in XML input):

      -A  Font size for feature labels (default 10).
      -c  Base position to center on when using -z option (default 1).
      -D  Font size for legends (default 8).
      -d  Density of tick marks, between 0 and 1.0 (default 1.0).
      -f  Output file format: png, jpg, svg, or svgz.
      -H  Height of map (default 700).
      -h  HTML file to create for image map functionality.
      -I  Allow labels to be drawn on inside of circle, T or F (default is T for zoomed maps and F for unzoomed).
      -L  Width of user-supplied legend png file (legend.png) to be referenced in html output.
      -p  Path to image file in HTML file created using -h (default is -o value).
      -r  Remove legends, T or F (default F).
      -R  Remove feature labels, T or F (default F).
      -U  Font size for sequence ruler (default 8).
      -u  Include overlib.js calls for mouseover labels for png and jpg image maps in html output, T or F (default T).
      -W  Width of map (default 700).
      -z  Zoom multiplier (default 1).

    example usage:

      java -jar cgview.jar -i test.xml -o map.png -f png

CREATE A NAVIGABLE SERIES OF LINKED MAP IMAGES:

  usage:

    java -jar cgview.jar -i <file> -s <directory> [Options]

    required arguments:

      -i  Input file in CGView XML or TAB format.
      -s  Output directory for image series.

    optional arguments (when used these override corresponding values specified in XML input):

      -A  Font size for feature labels (default 10).
      -D  Font size for legends (default 8).
      -e  Exclude SVG output from image series, T or F (default F).
      -H  Height of map (default 700).
      -I  Allow labels to be drawn on inside of circle, T or F (default is T for zoomed maps and F for unzoomed maps).
      -L  Width of user-supplied legend png file (legend.png) to be referenced in html output.
      -r  Remove legends, T or F (default F).
      -U  Font size for sequence ruler (default 8).
      -u  Include overlib.js for mouseover labels for png and jpg image maps in html output, T or F (default T).
      -W  Width of map (default 700).
      -x  Zoom multipliers to use, comma-separated (default is 1,6,36).

    example usage:

      java -jar cgview.jar -i test.xml -s image_series

If cgview.jar exits with Exception in thread "main" java.lang.OutOfMemoryError: Java heap space, use the -Xmx option to increase the memory allocation pool. For example, use the following command:

java -jar -Xmx2000m cgview.jar -i test.xml -o map.png -f png

Downloading CGView

The executable cgview.jar with dependencies included can be downloaded here.

To test cgview.jar on your system you can try the following:

wget https://paulstothard.github.io/cgview/xml_sample/overview.xml
java -jar cgview.jar -i overview.xml -o map.png

Building CGView

cgview.jar can be built from project source code using Apache Maven.

First clone the cgview repository and switch to the project directory:

git clone git@github.com:paulstothard/cgview.git
cd cgview

Build cgview.jar using mvn package:

mvn package

Alternatively, an included build.sh script can be used to execute mvn package and to run additional tests:

./build.sh

The build process should create several CGView maps in the test_maps directory and updated API documentation and jar files in the targets directory.

cgview_xml_builder.pl

The cgview_xml_builder.pl script can be used to generate XML input for cgview.jar from DNA sequence files. See the included README.md file for information on usage and required Perl modules.