Part A: Setting up the assembly in SeqMan NGen

In this part of the tutorial, you will simply read the steps but won’t follow them yourself. No data are provided, as the data set used is 16 GB in size.

1. Launch SeqMan NGen and choose New Assembly.

2. In the Workflow screen, choose Variant Analysis / Resequencing on the left. On the right, choose the NGS-Based workflow Whole genome.

3. In the Reference Sequence screen, click Download Genome Package.

Select Homo sapiens build GRCh38.p7 and press Select.

4. Check the box next to BED file and then use Browse to upload NexteraRapidCapture_Exome_TargetedRegions_v1.2Used.bed. Click Next.

5. In the Input Sequences screen, change the Experiment setup to Multi-sample. Click Add Folder and add FC1_NA12878_01 (daughter). Repeat twice to add FC1_NA12891_02 (father) and FC1_NA12892_03 (mother). Click Next.

6. In the Set Up Experiments screen, do not check any of the boxes. Click Next.

7. In the Assembly Options screen, click Next.

8. In the Analysis Options screen, click Set Experiment Genders. Select Female for the mother, Male for the father and Female for the daughter. Click OK. Check the box next to Import Variant Annotation Database. This will provide a highly enriched source of annotations for genes and other items of interest. Click Next.

9. In the Assembly Output screen, type in a Project name of CEPH Trio. Use Browse to select a writable location for the results. Click Next.

10. In the Run Assembly Project screen, note that the assembly requires about 1.5TB of disk space for temporary files. The recommendation is to run the assembly on the cloud.

Click the link “Run 4 assemblies on the cloud.” (The number of cloud assemblies needed is usually the number of samples plus one). The assemblies take about 3.5 hours to run on the cloud.

Proceed to Part B. Analyzing the results in ArrayStar.