Assembly conflicts and resolution
Bionano’s hybrid scaffolding pipeline detects and resolves chimeric joins, which are typically formed when short reads, molecules, or paired-end inserts are unable to span across long DNA repeats. The errors appear as conflicting junctions in the alignment between the Bionano map and NGS assemblies.
When Bionano’s hybrid scaffolding pipeline detects a conflict, it analyzes the single-molecule data that underlies the Bionano map and assesses which assembly is incorrectly formed. If the Bionano map has long molecule support at the conflict junction, the sequence contig is automatically cut, removing the putative chimeric join.
If it does not have strong molecule support, then the Bionano map is automatically cut. The cuts can be inspected and decisions manually corrected, after which all contigs and maps will be re-scaffolded.