Unipro UGENE Online User Manual v. 1.31
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Besides selecting an appropriate package for your operating system (Windows, macOS, or Linux; 32 or 64 bit), you should take into account the following considerations.

Should I download standard, full, or NGS package?
Tip

In most cases, the full package is the best choice. Exceptions are:

  • Use the standard package, if:
    • You're going to use only basic UGENE features and don't want to waste Internet traffic
    • You have limited disk space
  • Use the NGS package, if:

Explanation of the tip above: Some tools are embedded into UGENE as external. To be launched from the UGENE graphical interface, an external tool needs a corresponding executable file. The list of the external tools can be found on this page.

The standard package does not include the tools, whereas the full package 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.

Info

In 2013 we worked on extending of the UGENE NGS framework with three popular 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 out of the box. However, it appears that the first two pipelines are also available out of the box in the full UGENE package.

The work was supported by grant RUB1-31097-NO-12 from NIAID.

I have Windows. Should I download installer package or portable zip bundle?

If you have administrative rights on Windows, use the installer package. It will make integration with your Windows system tighter. For example, it will add associations for bioinformatics formats supported by UGENE, so that corresponding files are opened in it by default.

I have Linux. Which package should I use?

If your Linux is not Ubuntu or Fedora, you can use the installer package too. Otherwise, for more tight integration with the systems, you can install UGENE from corresponding repositories, following these guides:

...

The following package types are currently available:

  • Online Installer: if the Internet connection is available on the target computer, it is recommended to use this type of package. The installation wizard allows one to add required components or update them, when a new UGENE version is released.
  • Standard Package: the package includes UGENE main executables, embedded tools, sample data, etc.
  • Full Package: the same as in the Standard Package + external tools (including tools for NGS data analysis) – this package is recommended for offline installation.
  • NGS Package: the same as in the Full Package + ChIP-Seq data analysis additions (RScript, reference data)

Warning

The number of package types will be decreased in the next releases.

Also, different package delivery types are available depending on the operating system.