To follow the whole genome reference-guided workflow, also called the variant analysis workflow, make the following selections in the SeqMan NGen wizard:

  • (optional) In the Input Reference Sequences screen, use the check box(ex) and *Browse button(s) to import BED and/or VCF files.
  • (multiple genomes only) In the Input Sequence Files and Define Experiments or Individual Replicates screen, check the box Multi-sample data. If you also wish to run each data set as a separate assembly, check Run as separate assemblies.
  • In the Assembly Options screen, select the desired variant detection options.

For information on special types of whole genome reference-guided workflows, see Create an assembly to use in the ‘SNP to Structure’ workflow and Filter based on ‘P not Ref’.


These two brief videos all contain demonstrations of the whole genome reference-guided workflow. The upper video is for single genome assembly, and the lower video is for multiple genome assembly.


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