Order contigs and close gaps for de novo assembly

To order contigs and close gaps in a de novo .sqd assembly:

• SeqMan Pro – Provides a primer walking feature (Contig > Primer Walk) to locate primers that can drive the closure of gaps or to fill in low coverage areas. Results appear in the Alignment view and the Primer Walking report.

• SeqMan Ultra – Uses a three step process to create an enhanced template that can be used in future SeqMan NGen assemblies.
  
  
  1. Order contigs into scaffolds using Contig > Order Contigs or Contig > New Scaffold.
     
     
  2. Look for BLAST sequence matches using Search > Search.
     
     
  3. Use Contig > Add Sequences to Close Gap to align a sequence match with the existing assembly to close a gap between two contigs.
     
     
     
     

For step-by-step instructions, watch the video below or see this help topic.