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 Variant and Rare Variant Pipeline (Bionano Access v1.4)

Name Date Size Dataset
NA12878 (DLS, Structural Variant)December 4, 20193.13 GBDownload
SKBR3 (DLS, Structural Variant)December 4, 20199.4 GBDownload
SKBR3 (DLS, Rare Variant Pipeline)December 4, 20194.53 GBDownload

Structural Variation Training Datasets (Bionano Access)

Name Date Size Dataset
GM09888 (DLS)May 2, 20182.5 GBDownload
GM08331 (DLS)May 2, 20182.5 GBDownload
GM06226 (DLS)May 2, 20182.5 GBDownload
GM11428 (DLS)May 2, 20182.5 GBDownload
GM24143 (DLS)April 18, 20182.6 GBDownload
GM24149 (DLS)April 18, 20182.2 GBDownload
GM24385 (DLS)April 18, 20182.7 GBDownload
NA12878 (BSPQI)August 28, 20172.5 GBDownload
NA12878 (BSSSI)August 28, 20172.0 GBDownload

NA12878 genome was mapped using BSPQI and BSSSI nicking enzymes on the Saphyr system. Nickase genome map assembly, alignments, and structural variation calling was generated using Bionano Solve v3.1 (nickase). Visualization of the assembly report, molecules to maps alignment, and structural variation alignment to hg19 is done using Bionano Access v1.1 (nickase) and v1.2 (DLS).

Hybrid Scaffold Training DataSets (Bionano Access)

Name Date Size Dataset
NA12878 DLE-1 (PACBIO)May 24, 20182.5 GBDownload
NA12878 BSPQI (PACBIO)August 28, 20173.6 GBDownload
NA12878 2-Enzyme BSPQI and BSSSI (PACBIO)August 28, 20172.6 GBDownload

NA12878 genome was hybrid scaffolded using direct labeling enzyme (DLE-1), single nicking enzyme (BSPQI) or two nicking enzyme (BSPQI and BSSSI) genome map assemblies for PacBio input sequence assembly using Bionano Solve v3.1. 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 v1.1.

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)