The Choose Assembly Workflow dialog lets you select from a variety of workflow types divided into categories.

Once you make a selection, SeqMan NGen will populate the rest of the wizard with appropriate default parameters for your project. For example, your selection in this screen determines which assembly types are enabled in the next screen, entitled Choose Assembly Type, as shown in the table below.

This selection in Choose Assembly Workflow… …enables these options in Choose Assembly Type
Reference based – normal workflows Reference based with host removal De Novo De Novo with host removal Reference-guided with gap closure Reference-guided – special workflows Variant Calling Sanger Validation
Whole genome x x x x x
Exome and gene Panel x x x
Transcriptome/RNA-Seq x x
ChIP-Seq x x
miRNA x x
Metagenomics/population assembly x x x x
Viral-host integration x
Merge existing assemblies from same or different workflows (local users only) Combines existing .assembly packages from one or more workflows (e.g., RNA-Seq, ChIP-Seq, miRNA, Variants) into a single ArrayStar-readable project.
Rerun analysis of existing assemblies (local users only) Reanalyzes existing .assembly packages from one or more workflows and puts them into a single ArrayStar-readable project. Reanalysis is indicated, for example, after adding a new replicate, changing the normalization method, or adding VAD information. All the projects must have been assembled against the same reference sequence(s).

Once you are finished, click Next > to continue to the next wizard screen.

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