SeqMan NGen and SeqMan Ultra are two applications that work together to assemble and analyze both Sanger and NGS sequencing data. SeqMan NGen is the application that assembles and aligns the data, and is fully integrated in SeqMan Ultra so that you can go from streamlined project setup to finished assembly all in one application. SeqMan Ultra is one of the sequence assembly tools that allows you to analyze and edit the assembly produced by SeqMan NGen. (Additional applications within Lasergene Genomics are available for analyzing NGS projects and more complex Sanger assemblies).

SeqMan Ultra is the new face of SeqMan Pro, our longstanding sequence assembly software application, complete with a new modern, intuitive interface, as well as lots of performance improvements under the hood. SeqMan Ultra is a 64-bit application, which means when compared to the 32-bit SeqMan Pro application, it offers faster project opening, better performance for analyzing large files, increased capacity, and compatibility with macOS 10.15.  SeqMan Pro will still be available in Lasergene 17, but will eventually be completely replaced by SeqMan Ultra.

A known sequence can be used as a backbone/template/reference sequence upon which to build your sequence assembly. This lets you perform the assembly with lower average sequence coverage, thus saving a substantial amount of sequencing effort. Simply choose a reference-guided workflow when you set up your project, and you will be prompted to input a reference sequence.  If no reference sequence is available for your organism, try using one from a closely-related organism.

There are several options for organizing contigs in an assembly. If your input data is paired, you can use Contig>Order Contigs to automatically create scaffolds based on the paired data. You can also select contigs and use Contig>New Scaffold to manually create scaffolds or simply drag and drop contigs to reposition in the Explorer panel.  If you use the Hybrid reference-guided/de novo assembly workflow, contigs will automatically be placed in scaffolds based on the reference positions.

Select two or more contigs in the Explorer panel and use Contig>Align contigs end to end to align a multiple contigs to each other. If your contigs are in a scaffold, this alignment will preserve the position within the scaffold and greatly reduce the chance for misaligning contigs at repetitive elements. You can also manually align contigs using Contig>Force Join if you know that two contigs should be merged, but there is insufficient overlap for successful alignment.

From SeqMan Ultra, select Contig > Export Consensus and choose from the following options:

• Single File – all selected contigs are saved in a single file.
• Multiple Files – each selected contig is saved as a separate file.

Yes, you can easily export an image of your assembly for collaboration or publication in PDF, Bitmap, or PPT format by selecting File>Export Image>Alignment.

selecting File>Export Image>Alignment.

Yes, you can easily export an image of your assembly for collaboration or publication in PDF, Bitmap, or PPT format by selecting File>Export Image>Alignment.