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

cgview 0.0.20100111                               November 2015                                        CGVIEW(1)