If you are performing a non-Cloud assembly and a Download Genome Package is not available in the Input Files screen, you may download and extract the package manually.
To download a genome package:
Go to DNASTAR’s Genome Template Packages web page and download a free template package with the genome of interest. Each package contains the template sequence, annotations, and associated dbSNP linking information.
Downloaded genome packages are saved on your computer as ZIP files, and must be extracted prior to use.
To extract a downloaded genome package:
•On Macintosh: Double-click on the ZIP file. The files will be automatically extracted via the Archive Utility.
•On Windows 7 & Windows 8: 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.
See Automatically Downloading and Adding Genome Template Packages for instructions on adding the genome package to SeqMan NGen.
Note 1: 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 2: 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.