Add a genome template from DNASTAR

If your workflow includes the Reference Sequence or Set Contaminant screen, you must add at least one reference sequence, biome genome, or genome template before proceeding.

Curated and up-to-date DNASTAR genome template packages are available for common model organisms. Each template package contains template sequence, annotations, and database linking information. If you wish to use DNASTAR’s database association features (e.g., dbSNP, GERP, and COSMIC), you must input one of these genome packages in the appropriate screen for your workflow.

To download and add a DNASTAR genome template:

1. Press Download Genome Package. If the button is disabled, see the first two bullet points below.

2. Select a package from the list.

3. If you are using Lasergene version 17.4 or earlier, use the Browse button to select a save location and Click Select. The package is saved with the extension .genometemplate and is also added to the list of reference files.
   
   If you are using version 17.5 or later, SeqMan NGen will automatically save the genome template package to a specific location. This can save you disc space in the future, as SeqMan NGen will know whether you have already downloaded a package and won’t download a duplicate of a package that is already on your computer.

To add a previously-saved DNASTAR genome template:

1. Press Add Genome Package.

2. Navigate to the location where you saved the automatically downloaded (or manually downloaded & extracted) package, and click Open.

After creating an assembly with a genome template, you can access dbSNP information as described in the following brief video:

Notes:

• The Add Genome Package and Download Genome Package buttons are disabled if you have already added files using the Add or Add Folder buttons.

• If you are performing a local assembly, there are some circumstances in which it is necessary to download and extract the package manually prior to using the wizard. To do this, go to DNASTAR’s Genome Template Packages web page and download a template package with the genome of interest. Downloaded genome packages are saved on your computer as ZIP files, and must be extracted prior to use. On Macintosh, double-click on the ZIP file. The files will be automatically extracted via the Archive Utility. On Windows, use any archive utility to extract the files. One method is to double-click on the ZIP file. In the ensuing Explorer window, click Extract all files from the top left. Choose a location for the files and select Extract.

• 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.

• Chromosome names are captured from genome template packages and used to assign contig IDs to entries from BED and Manifest files.

• 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.

• The Human Genome Package includes Chr 1-22, X, Y, MT and “Unlocated.” DNASTAR’s “Unlocated” contigs match GenBank’s “Unplaced sequence,” i.e., items specifically annotated as “Homo sapiens concatenated unplaced genomic contigs.”