The Run Assembly screen follows the Assembly Output screen and prompts you to specify a name for the project and a location in which to save temporary files. You can also review system memory information that will help you make an educated decision whether to assemble on your local computer or on the cloud.

  • The “Input information” section shows a quick overview regarding the size of the planned assembly, including the total length of the reference sequences, estimated size of the read files, and estimate coverage area.
  • Under “Temporary files,” the Location box shows any location previously specified for temporary files created during the run. If you have not previously specified a location, the box will be blank. To specify or change the location, use the Browse button or open your computer’s file explorer and drag and drop the directory in the Temporary file location box. SeqMan NGen will remember and use the temporary file location for future assemblies. Here are some tips regarding temporary files:

    • If possible, use an external hard drive as the temporary file location.

    • Never save the assembly output files or temporary files directly to the desktop, as the many intermediate files and folders created during assembly may hamper or prevent further computer operations. However, files may be saved to a folder on the desktop.

    • By default, most temporary files are deleted when the assembly is complete. Other files (e.g., [template_name].FasInfo.sqlite and [template_name].mer) may remain in the temporary file location in order to facilitate efficient reassembly of data in the future.

    • You do not need to specify a temporary file location when following a de novo or special reference-guided workflow.
  • The “Estimated requirements” section consists of two columns. The Estimate column shows the estimated Memory and Free disk space required for the current assembly to run without failure. The This computer and temporary files column shows the amount of memory and free disk space on your local computer. If either value on the left is larger than its equivalent on the right, we strongly recommend you run the assembly on the cloud. Unless you have an extremely powerful computer, most non-bacterial assemblies should be run on the cloud.
  • In the “Run assembly* section, click the link to Run assembly on this computer or Run assembly on the cloud. Base your decision on the “Estimated requirements” section above. If you choose to run on the cloud and are not already logged in, you will be prompted to log in to Cloud Assemblies.

    • If you choose Run assembly on this computer, you must wait for one assembly to finish before beginning another. Note that de novo projects require ample amounts of RAM, while most reference-guided assemblies require large amounts of CPU and free hard drive space. Unless you have an unusually powerful computer, local assembly is best reserved for small, reference-guided assembly projects.

    • If you choose Run assembly on the cloud, you can perform any number of SeqMan NGen assemblies simultaneously, without using up your computer’s resources. The assembly takes place on a powerful Amazon cloud computer, and output data are stored securely on the cloud. To try Cloud Assembly for free*, contact your DNASTAR representative to request free trial access and a secure data storage folder.


If you want to make changes to a screen before proceeding, click the screen name on the left of the wizard or choose < Back to return to the previous screen.

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