Animal Genome Research
Advancing animal genome research is crucial for feeding the world and maintaining healthy ecosystems. Mammalian 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 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 animal genome research.
- 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
- Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low CostBioRxiv 2017
- Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genomeNature Genetics 2017
- Improvement of the threespine stickleback (Gasterosteus aculeatus) genome using a Hi-C-based Proximity-Guided Assembly methodBioRxiv 2016