The following datasets are designed to be used with Bionano Access. For instructions on downloading and installing the latest versions of Bionano Access as well as importing data, please refer to the following Bionano Access installation and user guides.

Structural Variation Training Datasets (Bionano Access)

Name Date Size Dataset
NA12878 (BSPQI)March 29, 20172.5 GBDownload
NA12878 (BSSSI)March 29, 20172.0 GBDownload

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, 20172.6 GBDownload
NA12878 (PACBIO)March 29, 20172.6 GBDownload
NA12878 (SOAPdenovo)March 29, 20172.6 GBDownload

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.

The following datasets are designed to be used with IrysView. For instructions on downloading and installing the latest versions of IrysView as well as importing data, please see the IrysView Installation and Training Guide.

HYBRID SCAFFOLD TRAINING DATASET (IRYSVIEW)

Name Date Size Dataset
NA12878 and Hummingbird (2-step)April 12, 20161.0 GBDownload

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
YH1December 1, 20141.0 GBDownload

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)1October 1, 20141.72 GBDownload
NA24149 (Father)1December 1, 20141.92 GBDownload
NA24143 (Mother)1December 1, 20141.75 GBDownload

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)1July 1, 20141.72 GBDownload

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)1March 1, 20141.2 GBDownload

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)