This tutorial is written for those with a Cloud Assembly license, whether purchased or from a free trial. The sample file is the genome from a single strain of Salmonella bacteria. You don’t need to download any data to follow this tutorial, as it is provided in your Cloud Data Drive.

To perform the assembly:

  1. Launch SeqMan NGen. If SeqMan NGen is already open as the result of setting up a previous assembly, close it and open it again before starting the tutorial.
  1. In the Begin Project screen, select Assembly on the DNASTAR cloud. At the prompt, enter your Email and the Password sent when you purchased or requested free trials of DNASTAR Cloud Assembly. Press Next.
  1. In the Cloud Assembly screen, keep the default selection New cloud assembly and click Next.
  1. In the Choose Assembly Workflow screen, keep the default setting Whole genome and click Next.
  1. In the Choose Assembly Type screen, select De novo assembly and click Next.
  1. In the Input Sequence Files and Define Experiments or Individual Replicates screen:

    1. Press Cloud Demo Data.

    2. In the pop-up, select the row 4 Salmonella genome strains/strain 1 and click Select.

    3. Back in the wizard, select Illumina from the Read technology drop-down menu. Note that the box next to Paired-end data is checked automatically.

    4. Click Next.
  1. In the Read Options screen, keep all defaults and click Next.
  1. In the Assembly Options screen:

    1. In the Expected genome length box, type in 4600000 (i.e. a 46 followed by 5 zeros).

    2. Press Next.
  1. In the Assembly Output screen:

    1. Enter the project name Salmonella de novo.

    2. Press the Browse button to launch the DNASTAR Cloud Data Drive window:

      1. Within the Cloud Data Drive, press the Home tool ().

      2. If you see a folder named Assemblies, skip to Step iii. Otherwise, click the Create a new folder on the cloud tool on the top right. In the pop-up box, type in Assemblies and press Done.

      3. Single click on the Assemblies folder to select it, then press the green check mark in the bottom right corner of the DNASTAR Cloud Data Drive window.

    3. Back in the Assembly Output screen, press Next.
  1. In the “Your assembly is ready to begin” screen, press Start Assembly to begin the assembly.
  1. Assembly for this tutorial should take approximately 1-2 hours, and you can check the status of the assembly at any time. To begin another tutorial while this assembly is in progress, close the current instance of SeqMan NGen by pressing Next and Finish, then proceed to Cloud Assembly Tutorials 1, 5 or 6.
  1. When the Tutorial 3 assembly is complete, download only the 2GB file Assemblies/Salmonella de novo/Samonella de novo.sqd. Double-click on the file to open the project in SeqMan Pro. For analysis ideas, see Tutorial 2, Part B.

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