This tutorial is written for those with a Cloud Assembly license, whether purchased or from a free trial. In this tutorial, you will assemble two data files with human microbiome samples against DNASTAR’s Microbial genome database, which consists of over 3,500 microbial genomes from the National Center for Biotechnology Information (NCBI). 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, select Metagenomics / population assembly and click Next.
  1. In the Choose Assembly Type screen, keep the default setting Reference based assembly and click Next.
  1. In the Input Biome Genomes screen:

    1. Press the Add Genome Package button.

    2. In the pop-up, select Microbial Genome database 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 both rows beginning with Human gut microbiome 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 Assembly Options screen, select Do not calculate variants and press Next.
  1. In the Assembly Output screen:

    1. Enter the project name Human microbiome.

    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 hour, 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, 3 or 5.
  1. When the Tutorial 6 assembly is complete, download the ~300 kb files Assemblies/Microbiome/sample 1.7z/sample 1.7z-perTemplateResults.txt and Assemblies/Microbiome/sample 2.7z/sample 2.7z-perTemplateResults.txt. Open the files in Microsoft Excel or a similar spreadsheet application to view tables showing the counts of aligned reads to genome sequences.

If desired, you can also download the .assembly files and analyze them in SeqMan Pro as shown in the following video:

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