Bionano Datasets
Next-Generation Mapping (NGM) generated by the Bionano Irys® or Saphyr™ Systems enables researchers to more fully and accurately characterize the human genome. This webpage provides links to Bionano mapping data, de novo assemblies, and annotations of genomic variation to be used with our Bionano Access™ or IrysView® software.
We provide these datasets to enable the community to better understand and interact with NGM data.
For Bionano Access, directly import the compressed download.
For IrysView, import the “output” folder revealed by uncompressing the downloaded file using WinRAR or 7-Zip.
Structural Variation Training Datasets (Bionano Access)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA12878 (BSPQI) | March 29, 2017 | 2.5 GB | Download |
| NA12878 (BSSSI) | March 29, 2017 | 2.0 GB | Download |
NA12878 genome was mapped using both BSPQI and BSSSI nicking enzymes on the Saphyr system. Genome map assembly, alignments, and structural variation calling was generated using Bionano Solve v3.0. Visualization of the assembly report, molecules to maps alignment, and structural variation alignment to hg19 is done using Bionano Access v1.0.
Hybrid Scaffold Training DataSets (Bionano Access)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA12878 (DISCOVAR) | March 29, 2017 | 2.6 GB | Download |
| NA12878 (PACBIO) | March 29, 2017 | 2.6 GB | Download |
| NA12878 (SOAPdenovo) | March 29, 2017 | 2.6 GB | Download |
NA12878 genome was hybrid scaffolded using both BSPQI and BSSSI genome map assemblies for three different input sequence assemblies: DISCOVAR, PacBio, and SOAPdenovo. Two enzyme hybrid scaffold results were generated using Bionano Solve v3.0. Visualization of the hybrid scaffold report, alignment of maps to sequence along with conflict resolutions, and alignment of maps to sequence to hybrid scaffold is done using Bionano Access v1.0.
HYBRID SCAFFOLD TRAINING DATASET (IRYSVIEW)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA12878 and Hummingbird (2-step) | April 12, 2016 | 1.0 GB | Download |
The zip file in this directory contains the essential files needed to run the hybrid scaffold pipeline using IrysView 2.4 and IrysSolve 2.0
YH (IrysView)
| Name | Date | Size | Dataset |
|---|---|---|---|
| YH1 | December 1, 2014 | 1.0 GB | Download |
YH genome assembled and aligned against hg19 using IrysView 2.3, pipeline scripts v4125, and tools v4088
1Cao, H., et al. Rapid Detection of Structural Variation in a Human Genome using Nanochannel-based Genome Mapping Technology. Giga Science (2014); 3(December 2014): 34
Ashkenazi Trio (IrysView)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA24385 (Son)1 | October 1, 2014 | 1.72 GB | Download |
| NA24149 (Father)1 | December 1, 2014 | 1.92 GB | Download |
| NA24143 (Mother)1 | December 1, 2014 | 1.75 GB | Download |
Ashkenazi Father-Mother-Son trio from Personal Genome Project assembled and aligned against hg19 using IrysView 2.3, pipeline scripts v4125, and tools v4088
1 Zook, J., et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. BioRxiv (2015)
CEPH Trio (IrysView)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA12878 (Daughter)1 | July 1, 2014 | 1.72 GB | Download |
CEPH pedigree 1463 Father-Mother-Daughter trio assembled and aligned against hg19 using IrysView 2.3, pipeline scripts v4125, and tools v4088
1Pendleton, M., Sebra, R., et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods (2015); e3454
2Mak AC et al., Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays Genetics (2015)
Han Chinese Son (IrysView)
| Name | Date | Size | Dataset |
|---|---|---|---|
| NA24631 (Son)1 | March 1, 2014 | 1.2 GB | Download |
Han Chinese Son from Personal Genome Project assembled and aligned against hg19 using IrysView 2.3, pipeline scripts v4125, and tools v4088
1Zook, J., et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. BioRxiv (2015)