Animal Genome Research

Advancing animal genome research is crucial for feeding the world and maintaining healthy ecosystems. Most animal genomes are highly repetitive with large structural variations that sequencing-based tools alone cannot resolve. Bionano Saphyr™ offers hybrid scaffolding and structural variation discovery capabilities that are essential to overcoming these hurdles.

Generating high-quality finished animal genomes remains challenging. Assembly contiguity and accuracy is vital to driving discovery. Unlike next-generation sequencing (NGS), which is based on inferring genome structure information 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 assemblies to order and orient sequence fragments, identify and correct potential chimeric joins in the sequence assemblies, and estimate the gap size between adjacent sequences.

Bionano hybrid scaffolding considerably reduces the number of contigs found in initial NGS assemblies and improves contiguity up to 1000 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 500 bp to megabase pair lengths.

  • 99% sensitivity for homozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for heterozygous insertions/deletions larger than 500 base pairs
  • 95% sensitivity for balanced and unbalanced translocations larger than 50,000 base pairs
  • 99% sensitivity for inversions larger than 30,000 base pairs
  • 97% sensitivity for duplications larger than 30,000 base pairs

For mosaic samples or heterogeneous cancer samples, Saphyr detects all types of structural variants down to 5% Variant Allele Fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also detects repeats, copy number variants, and complex rearrangements.

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

Use Cases

  • Selective breeding – identify areas of biological interest for achieving desirable traits in livestock
  • Evolutionary biology – see the complete picture of how genomes have evolved and been reorganized
  • Disease discovery – call structural variations to identify variants of interest and their effect on genes and disease
  • Reference genome assembly – perform de novo assembly and scaffold assemblies generated by sequencing-based systems
Bionano genome maps help researchers assemble the most accurate animal reference genomes


Towards high quality reference assemblies for all vertebrate genomes
Bionano optical mapping, in combination with other sequencing-based technologies, to deliver accurate chromosome length genome assemblies.
Reference quality genomes of bats to illuminate the genomic determinants and evolution of unique adaptations in bats.


        White Papers
      • This white paper explains how Bionano whole genome imaging can make any sequence assembly up to 100 times more contiguous by scaffolding sequence contigs, and more exact by correcting errors. The new two-enzyme hybrid scaffold pipeline introduced here improves both aspects. It creates functional genomes at a low cost, no matter what your sequencing strategy is.


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