Bionano Datasets
This webpage provides links to optical genome mapping data generated with the Saphyr and analyzed using Bionano Access and Bionano Solve. Datasets are available for training and demonstration purposes, including de novo assemblies, rare variant analyses, and EnFocus FSHD job outputs. These datasets are to be used with our Bionano Access software.
The following datasets may be imported into Bionano Access for visualization, filtering, and exporting. 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.
To download, right-click and Save As. Import the archive directly into Bionano Access.
Molecules, De Novo Assembly, and Rare Variant Analysis (Bionano Access V1.6)
| Name |
Date |
Size |
Dataset |
| HCC2218 (Molecules) | April 1, 2021 | 3 GB | Download |
| HCC2218 (De Novo Assembly) | April 1, 2021 | 3.5 GB | Download |
| HCC2218 (Rare Variant Analysis) | April 1, 2021 | 2.7 GB | Download |
Structural Variant and Rare Variant Pipeline (Bionano Access v1.4)
| Name |
Date |
Size |
Dataset |
| NA12878 (DLS, Structural Variant) | December 4, 2019 | 3.13 GB | Download |
| SKBR3 (DLS, Structural Variant) | December 4, 2019 | 9.4 GB | Download |
| SKBR3 (DLS, Rare Variant Pipeline) | December 4, 2019 | 4.53 GB | Download |
FSHD Training Set (Bionano Access v1.5)
| Name |
Date |
Size |
Dataset |
| GM16348 (DLS, .bnx File) | February 27, 2020 | 1.09 GB | Download |
| GM16348 (DLS, FSHD Analysis) | December 12, 2019 | 151 MB | Download |
Structural Variation Training Datasets (Bionano Access v 1.1)
| Name |
Date |
Size |
Dataset |
| GM09888 (DLS) | May 2, 2018 | 2.5 GB | Download |
| GM08331 (DLS) | May 2, 2018 | 2.5 GB | Download |
| GM06226 (DLS) | May 2, 2018 | 2.5 GB | Download |
| GM11428 (DLS) | May 2, 2018 | 2.5 GB | Download |
| GM24143 (DLS) | April 18, 2018 | 2.6 GB | Download |
| GM24149 (DLS) | April 18, 2018 | 2.2 GB | Download |
| GM24385 (DLS) | April 18, 2018 | 2.7 GB | Download |
| NA12878 (BSPQI) | August 28, 2017 | 2.5 GB | Download |
| NA12878 (BSSSI) | August 28, 2017 | 2.0 GB | Download |
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, 2018 | 2.5 GB | Download |
| NA12878 BSPQI (PACBIO) | August 28, 2017 | 3.6 GB | Download |
| NA12878 2-Enzyme BSPQI and BSSSI (PACBIO) | August 28, 2017 | 2.6 GB | Download |
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.
