Downloaded genome packages are saved on your computer as ZIP files, and must be extracted prior to use.
To extract the genome package:
• On Macintosh: Double-click on the ZIP file. The files will be automatically extracted via the Archive Utility.
• On Windows Vista or Windows 7: 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.
To add the genome package to SeqMan NGen:
SeqMan NGen does not appear in the Ubuntu Software Center's Installed Software list. This issue has been observed on Linux machines running Ubuntu 10.04, but may occur with other versions, as well.
The issue can be resolved using either of the methods below:
Perform at least one SeqMan NGen assembly prior to opening the Ubuntu Software Center.
Open the Synaptic Package Center by choosing SYSTEM > Administration > Synaptic Package Manager. Search for SeqMan NGen. After confirming the presence of SeqMan NGen, close the Package Manager and re-launch the Software Center.
After using either method, SeqMan NGen Linux should now be listed in the Software Center's Installed Software list.
Assembly Options dialog > Advanced Assembly Options button > SNP tab > SNP calculation method drop-down menu = Diploid bayesian or Haploid bayesian.
Recalculate SNPs > SNP Options button > SNP calculation method drop-down menu = Diploid bayesian or Haploid bayesian.
When you perform the identical assembly in SeqMan NGen versions 3.0 and 3.1, some assembly statistics may appear “worse” in the newer version. This is actually due to an improvement in SeqMan NGen’s calculation algorithm. The criterion for calculating contig length is now more stringent and excludes positions that contain more than 50% gaps. In general, this causes the average contig length in version 3.1 to be shorter than in version 3.0. The statistics that may be affected by this improvement include:
Contigs to Reach Genome Length
Average Lengths: Contigs
This change in the algorithm assures that you will get the most accurate assembly possible.
1. Use the wizard to create and run the script.
2. At the command-line, specify the path to the application followed by the path to the script.