The following tutorials cover several of the most popular workflows in SeqMan NGen. Each tutorial begins with setting up and running an assembly in SeqMan NGen, then proceeds to other Lasergene applications for downstream analysis.

The upper part of this topic, including the table, pertains to tutorials that can be run locally or using Cloud Assemblies. The lower part of the topic with the bulleted list shows tutorials that can be run only using Cloud Assemblies.

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Data for each tutorial below can be downloaded for free for assembly on a local computer. Within each tutorial is a direct link for downloading the data in archived (.zip) format.

Tutorial
Number
Tutorial
Name
Assembly
Part A
Downstream Analysis
Part B
Additional Analysis
Part C
1 Whole genome reference-guided workflow with analysis in SeqMan Pro

For another whole genome reference-guided workflow, see Tutorial 6, below.
Setting up and running a reference-guided assembly in SeqMan NGen Analyzing assembly results in SeqMan Pro
2 Whole genome de novo workflow with analysis in SeqMan Pro Setting up and running a de novo assembly in SeqMan NGen Analyzing results in SeqMan Pro
3 RNA-Seq reference-guided workflow with analysis in ArrayStar Setting up a referenced-guided RNA-Seq project in SeqMan NGen Analyzing the RNA-Seq results in ArrayStar
4 RNA-Seq de novo transcriptome workflow with analysis in SeqMan Pro Setting up and running an RNA-Seq de novo transcriptome assembly in SeqMan NGen Viewing transcripts in SeqMan Pro
5 Validation control accuracy workflow with analysis in ArrayStar Creating the validation assembly in SeqMan NGen Running the validation analysis in ArrayStar
6 Copy number variation (CNV) workflow with analysis in ArrayStar and GenVision Pro Setting up the CNV project in SeqMan NGen Finding a putative duplication in the reference sequence using ArrayStar Confirming the duplication using GenVision Pro
7 Sanger validation workflow with analysis in SeqMan Pro Setting up and running the assembly in SeqMan NGen Confirming non-Sanger reads in SeqMan Pro
8 ChIP-Seq workflow with analysis in ArrayStar Creating the ChIP-Seq assembly in SeqMan NGen Analyzing the ChIP-Seq results in ArrayStar

The following six tutorials are designed for anyone with a Cloud Assemblies license (including a free trial license) and can be followed in any order. All tutorial data is instantly accessible at the touch of a button, so there’s no need to download anything before starting the tutorials.

1: Whole genome reference-guided workflow
2: Whole genome reference-guided workflow
3: Whole genome de novo workflow
4: RNA-Seq reference-guided workflow
5: RNA-Seq de novo workflow
6: Metagenomics workflow

One of the advantages of Cloud Assembly is that you can run multiple assemblies at the same time. For example, you could start the Tutorial 1 assembly and quickly follow up by starting the assemblies for Tutorials 3, 5 and 6. The assemblies will run simultaneously on the cloud without using up any of your local computer resources. Note that tutorials 2 and 4 contain very large data sets and should be run one at a time, when no other assemblies are taking place.

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