Plant Genome Research

Short-read technologies typically fail to span long repeat regions or disambiguate different copies of interspersed repeats, resulting in limited contig length, introduction of chimeric joins and other assembly errors. Unlike next-generation sequencing (NGS), which algorithmically infers structural variations from fragmented DNA data, Bionano optical genome mapping directly observes long DNA molecules by linearizing and imaging DNA in its native state using massively parallel NanoChannels.

De novo Saphyr genome maps can be integrated with sequence assembly to order and orient sequence fragments, identify and correct potential chimeric joins in the sequence assembly, and estimate the gap size between adjacent sequences.

Bionano hybrid scaffolding considerably reduces the number of contigs found in the initial NGS assembly and improves contiguity up to 100 times over NGS-based approaches alone.

The combination of Bionano maps with sequencing data improves assembly accuracy and quality while reducing the need for deep sequencing coverage. This improved contiguity significantly lowers costs associated with assembling reference genomes.

Saphyr also offers unparalleled sensitivity for large structural variations from 1,000 bp to megabase pair lengths.

• 99% sensitivity for large homozygous insertions and deletions
• 87% sensitivity for large heterozygous insertions and deletions
• 98% sensitivity for translocations
• 98% sensitivity for inversions

Saphyr provides this performance with a false positive rate of less than 3%. Saphyr also detects inversions, repeats, copy number variants and complex rearrangements.

See below for publications, white papers and other resources regarding Bionano genome mapping in plant genome research.