Anyone knows a java application for the Circos ideogram/karyogram viewer? I would like to generate visual results from my NGS data, but I am not a C+ programmer and would need an easier platform.
You don't need C++ to generate an ideogram in CIRCOS. CIRCOS itself was written in Perl and can be installed on a *nix or Windows machine. Once installed on a system, all you need is a series of text files to generate the ideogram and overlay your NGS data on it. There is a fairly detailed tutorial on how to generate the ideograms here: http://circos.ca/documentation/tutorials/
There is a little bit of a learning curve to create the configuration file for Circos but its not too complicated overall.