Besides selecting an appropriate package for your operating system (Windows, Mac OS XmacOS, or Linux; 32 or 64 bit), you should take into account the following considerations.
Should I download standard, full, or NGS package?
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In most cases, the full package is the best choice. Exceptions are:
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The standard package does not include the tools, whereas the full package include includes all the required tools.
The NGS package, besides containing the external tools, contains sample data for the Cistrome pipeline (hg19 genome, reference genes, etc.), so you can run it out of the box.
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If you have administrative rights on Windows, use the installer package. It will make integration with your Windows system more tighttighter. For example, it will add associations for bioinformatics formats supported by UGENE, so that corresponding files are opened in it by default.
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