This tutorial is written for those with a Cloud Assembly license, whether purchased or from a free trial. Samples consist of four strains of Salmonella bacteria which are assembled against DNASTAR’s Salmonella genome template package. 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, 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, keep the default setting Reference based assembly – normal workflow and click Next.
  1. In the Input Reference Sequences screen:

    1. Press the Add Genome Package button.

    2. In the pop-up, select Salmonella enterica Heidelberg SL476 and click Select.

    3. Back in the wizard, press Next.
  1. In the Input Sequence Files and Define Experiments or Individual Replicates screen:

    1. Press Cloud Demo Data.

    2. In the pop-up, use Shift+click to select the four rows beginning with 4 Salmonella genome strains and click Select.

    3. Back in the wizard, click the Auto Name button.

    4. Select Illumina from the Read technology drop-down menu. Note that the Paired-end data and Multi-sample data boxes are checked automatically.

    5. Click Next.
  1. In the Set Up Experiments screen, leave all boxes unchecked and click Next.
  1. In the Assembly Options screen:

    1. Select Haploid as the Variant detection mode.

    2. If present, remove the check mark next to Calculate copy number variation to enable faster assembly.

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

    1. Enter the project name Salmonella strains.

    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 1.5 hours, and you can check the status of the assembly at any time. Due to the size of the Tutorial 2 data set, we do not recommend starting another tutorial until the current assembly has finished.
  1. When the Tutorial 2 assembly is complete, compare the different Salmonella strains by downloading the 1.6 GB Assemblies/Salmonella strains project folder and double-clicking on the file Salmonella strains/Salmonella strains-qng/Salmonella strains.astar to analyze the results in ArrayStar.

For a video showing a similar analysis using bacterial strains, see the following video (which begins with the analysis at 2:00):

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