The Bionano Genome Imaging workflow starts with mega-base size DNA isolation. A single enzymatic reaction labels the genome at a specific sequence motif occurring approximately 15 times per 100 kbp in the human genome. The long, labeled DNA molecules are linearized in nanochannel arrays on a Saphyr chip® and imaged in an extremely high throughput, automated manner by the Saphyr® Genome Imaging Instrument. Using pairwise alignments, the molecules are assembled into local maps or whole genome de novo assemblies. Changes in patterning or spacing of the labels are detected automatically, genome wide, to call all structural variants.

The de novo assembled Bionano optical maps can be integrated with a sequence assembly to order and orient sequence fragments accurately, identify and correct potential chimeric joins in the sequence assembly, and estimate the gap size between adjacent contigs. Sequence contigs are aligned to de novo Bionano optical maps using Bionano Solve Software. Hybrid scaffolds are generated by resolving conflicts between sequence contigs and Bionano maps and can be exported as FASTA and AGP files. This pipeline is fully integrated with Bionano Access™ which provides a convenient interface for running the Hybrid Scaffold pipeline and viewing scaffolding results.

Hi-C-based scaffolding tools have become popular because of their ability to link even the shortest sequence contigs into chromosome-length scaffolds. However, this highly stochastic method based on the statistical interpretation of the frequency of chromatin cross-links within the nucleus shows a high number of errors in order and orientation of the contigs. Bionano maps can help identify and correct these errors.

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.