Good scaffolds matter.

Validating results is a mandatory step in any project.
ScaMPI assist the user in two kinds of validation:
1) Contig validation - using MP reads to assess their correctness, breaking misassemblieas apart.
2) Scaffolding validation - using long insert (eg BAC ends) molecules to assess scaffolding correctness.

Validation

Contig validation

Misassemblies in contigs will lead to major problems in scaffolding. Most chimeric contigs can be spotted using mate paired reads, i.e. analyzing the physical coverage. ScaMPI provides a module for this step that breaks contigs when their physical coverage drops.

Scaffolds validation...

A module for BAC ends alignment and scaffolding validation will report how many bases of the genome are validated. For each scaffold a graphical representation is produces (see figure).

...and extension

This tool will also report scaffolds that could be joined together. Via the interface it is possibile to join two scaffolds, providing their correct mutual orientation.

Telomeres as a hint

When performing the telomere identification, finding all the telomeres at the end of a scaffold is a hint of peritelomeric regions correctly assigned (as they are a common cause of misassemblies).