Depending on the workflow, several SeqMan NGen wizard screens may allow you to download and/or add DNASTAR genome template packages. If you wish to use DNASTAR's database association features, you must input one of these genome packages in the appropriate screen for your workflow.
Each template package contains template sequence, annotations, and associated dbSNP linking information.
To add template packages:
•Local assemblies – Step 1) If you have previously downloaded a genome package to your local computer, skip to Step 2. Otherwise, if a Download Genome Packages button is present, click the button, select a package from the list, and click Select. When prompted, choose a location in which to save the package. When the download finishes, click OK. If the button is not present, instead follow the procedure in Manually Downloading and Extracting a Genome Package. Step 2) Click Add Genome Package, navigate to the location where you saved the automatically downloaded (or manually downloaded & extracted) package, and click Open.
•Cloud assemblies – Click Add Genome Package, select a package from the list, and click Select.
In both cases, the genome template package now appears in the large white box on the left of the dialog.
Notes about downloading and adding template packages:
•The Add Genome Package and Download Genome Package buttons are disabled if you have already added files using the Add or Add Folder buttons.
•SeqMan NGen can read and produce output using a variety of common chromosome naming conventions, including “chr1” and “ch1,” as well as Arabic and Roman numerals. Chromosome names are captured from genome template packages and used to assign contig IDs to entries from BED, VCF and manifest files. (Note that manifest files are typically used to represent coordinates of regions that were captured in procedures, such as exon capture performed prior to sequencing.)
•In the human genome template packages provided by DNASTAR, the “unlocated contig” is actually a concatenated, multi-sequence contig containing the alternate loci sequences. These loci are used for large regions where the human population contains variation so divergent that it cannot be adequately described by simple substitutions and small indels. Examples of these regions include the LRC/KIR complex on chromosome 19 and the MHC on chromosome 6.