NAME¶
cgview - Circular Genome Viewer
SYNOPSIS¶
cgview [OPTIONS] ...
DESCRIPTION¶
CGView is a Java package for generating high quality, zoomable maps of circular
genomes. Its primary purpose is to serve as a component of sequence annotation
pipelines, as a means of generating visual output suitable for the web.
Feature information and rendering options are supplied to the program using an
XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input
into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete
with labels, a title, legends, and footnotes. In addition to the default full
view map, the program can generate a series of hyperlinked maps showing
expanded views. The linked maps can be explored using any web browser,
allowing rapid genome browsing, and facilitating data sharing. The feature
labels in maps can be hyperlinked to external resources, allowing CGView maps
to be integrated with existing web site content or databases.
OPTIONS¶
- -A <integer> Specifies a label font size.
- -c <integer> Specifies the base to center on when
zooming.
- -D <integer> Specifies a legend font size.
- -d <real> Specifies tick density, between 0 and 1.0. Default
is 1.0.
- -E <boolean> Whether or not to embed vector-based text in SVG
output.
- -e <boolean> Whether or not to exclude SVG output from image
series.
- -f <format> The format of the output: PNG, JPG, SVG, or
SVGZ.
- -h <file> HTML file to create.
- -H <integer> The height of the map.
- -i <file> The input file to parse.
- -I <boolean> Whether or not to draw labels on the inside of
the backbone circle.
- -L <integer> The width of an external legend.
- -o <file> The image file to create.
- -p <path> The path to the image file in the HTML file created
using the -h option.
- -r <boolean> Whether or not to remove legends.
- -R <boolean> Whether or not to remove labels.
- -s <directory> Directory to receive an image series.
- -S <boolean> Whether or not to reference external stylesheet
in HTML output.
- -u <boolean> Whether or not to reference overlib.js in HTML
output.
- -U <integer> Specifies a sequence ruler font size.
- -W <integer> The width of the map.
- -x <string> Comma separated zoom values for image
series.
- -z <real> The factor to zoom in by.
EXAMPLES¶
cgview
-f png
-i cybercell.xml
-o my_picture.png
-h
view_image.html
cgview
-i cybercell.xml
-s directory_for_series
-e
true