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Besides selecting an appropriate package for your operating syst= em (Windows, Mac OS X, or Linux; 32 or 64 bit), you should take into accoun= t the following considerations.
In most cases the full package is the best choice.
Explanation of the tip above: Some tools are e= mbedded into UGENE as external. To be launched from the UGENE graphical int= erface, an external tool needs a corresponding executable file. The list of= the external tools can be found on this page.
Th= e standard package does not include the tools, whereas the full package inc= lude all the required tools.
The NGS package, besides containing the external tools, contains sample = data for the Cistr= ome pipeline (hg19 genome, reference genes, etc.), so you can run it ou= t of the box.
In 2013 we worked on extending of the UGENE NGS framework with three pop= ular pipelines for analyzing NGS data:
The NGS package was added as the result of this work. We decided to add = it as we want our users to be able to use all UGENE features o= ut of the box. However, it appears that the first two pipelines are also av= ailable out of the box in the full UGENE package.
The work was supported by grant RUB1-31097-NO-12 from NIAID.
If you have administrative rights on Windows, use the installer package.= It will make integration with your Windows system more tight. For example,= it will add associations for bioinformatics formats supported by UGENE,= so that corresponding files are opened in it by default.
If your Linux is not Ubuntu or Fedora, then universal binary packag= e is the only choice. Otherwise, for more tight integration with the system= s, you can install UGENE from corresponding repositories, following these g= uides:
Please note that the repositories may be updated a little later the offi= cial UGENE release date.