Welcome to the IPK visual analytics tool suite for barley genebank genomics
| Search more than 22,000 barley germplasm samples by passport and phenotypic data | |
| Visually explore hundreds of thousands of SNPs called against Morex V1, V2 and V3 | |
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Visualize and select germplasm on the interactive world map |
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Inspect genetic diversity via scatterplots of PCA and t-SNE dimensionality reduction |
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Inspect GWAS results with interactive Manhattan plots |
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Export of genotypic data in VCF files |
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Export of phenotypic data in ISA-Tab format |
| Order your barley accessions of interest directly from the IPK Genebank |
Please evaluate this de.NBI service! Give your feedback!2021
- 07.06.2021: The legacy SNP-Browser for Morex V1 has been removed
- 02.06.2021: The layout of the startpage was renewed
- 30.04.2021: Added SNP-Browser for Morex V3 referenced genotype panel with all 22626 BRIDGE genotypes
- 30.04.2021: Added BLAST-feature to SNP-Browsers for Morex V2 and V3
2020
- 15.11.2020: Added SNP-Browser for Morex V2 referenced genotype panel with all 22626 BRIDGE genotypes
- 15.11.2020: Major update of the SNP-Browser with new features: Display of SnpEff annotations, Local PCA, Display of per-SNP-metadata
- 25.02.2020: Added DOIs of germplasm origin genebank accession and descendant material (where available)
- 03.02.2020: Fixed bug in VCF export service
2019
- 07.11.2019: New feature added: new buttons in "Select Germplasm" page for filter search result by "Only germplasm with a photo" and "Only germplasm with phenotypic data"
- 05.11.2019: New feature added: MIAPPE-compliant ISA-Tab export of phenotypic data
- 17.07.2019: New feature added: "Genetic Distance Color Mapper" to colorize scatterplots by genetic distance to the reference genotype
- 10.07.2019: New feature added: "Phenotype Data Color Mapper" to map phenotypic traits on scatterplots and the worldmap
- 24.06.2019: Added column in germplasm search result table to show if phenotypic data is available for a germpplasm sample
- 20.06.2019: Added possibility to search for specific accession number prefixes on "Search Germplasm" page
2018
- 15.11.2018: Added a page "Germplasm collections" where one can see created collections in a datatables.
- 06.09.2018: Added a page "Germplasm details" where one can see passport data and phenotypic data of accessions.
- 10.04.2018: Added possibility to load core 1000, core 200 and core 50 set of accessions (in the tab "Select Germplasm")
- 29.03.2018: In addition to the unimputed SNP matrix, the imputed SNP matrix (basis for the GWAS) has also been added to the SNP Browser
- 27.03.2018: SNP Browser was improved with functionality to filter SNP's by either minor allele frequency, minor allele count, fraction of heterozygosity and/or fraction of missing calls
- 09.03.2018: In the "Manage your filters"-dialogue the defined filter sets can now be saved as a file and loaded again. With this feature a user can send his filter sets to a associates via E-Mail for collaborate work.
- 02.03.2018: New feature added: Link between GWAS plot and SNP Browser (click on a SNP position in GWAS-plot and you get the corresponding position in the SNP Browser on your screen)
- 22.02.2018: New feature added: PCA Scatterplot Matrix in the tab "PCA Matrix"
2017
- 08.11.2017: Added "Institute Code" and "Donor Institute Code" in filter result datatable with links to www.fao.org
- 02.11.2017: Added new tab with a parallel coordinate plot of the first ten principle components
- 27.10.2017: A photo of the accession (if available) is now displayed as a tooltip when hovering over the Photo-link in the filter result datatable
- 26.10.2017: Ability to switch off spike and grain filter panel; filtered accessions are now displayed in a datatable below filter panels
- 20.10.2017: New tab "Statistics" with world map to visualize the number of accessions per country
- 17.10.2017: Possibility to change dot transparency in PCA plots with a slider for each named filter set
- 16.10.2017: Possibility to change filter set color afterwards by clicking on the appropriate color swatch in the modal dialog that opens after click on "Show list of filters"-button
- 22,626 barley germplasm samples
- 9,527 samples with phenotypic data
- 6,162 samples with a spike photo
- 2,862 samples with geographic coordinates
- 15 phenotypic traits of spike, awn and seeds
- 5 traits as GWAS results
- Available SNP sets as SNP-Browser:
Reference genome # SNPs # Genes Morex V1 171,263 39,734 Morex V2 775,283 63,658 Morex V3 1,052,403 81,687
Citations keep this service running. If you use BRIDGE please cite:
König P, Beier S, Basterrechea M, Schüler D, Arend D, Mascher M, Stein N, Scholz U and Lange M. BRIDGE - A Visual Analytics Web Tool for Barley Genebank Genomics. Frontiers in Plant Science (2020) doi.org/10.3389/fpls.2020.00701
Milner, S.G., Jost, M., Taketa, S. et al. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 51, 319–326 (2019). doi.org/10.1038/s41588-018-0266-x
Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Simková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. The Plant Cell (2021). doi.org/10.1093/plcell/koab077
Monat, C., Padmarasu, S., Lux, T. et al. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 20, 284 (2019). doi.org/10.1186/s13059-019-1899-5
Mascher, M., Gundlach, H., Himmelbach, A. et al. A chromosome conformation capture ordered sequence of the barley genome. Nature 544, 427–433 (2017). doi.org/10.1038/nature22043
Beier, S., Himmelbach, A., Colmsee, C. et al. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.. Sci Data 4, 170044 (2017). doi.org/10.1038/sdata.2017.44
germplasm samples were found with your given search criterions.
Loading tabular data...
Loading...| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 |
| 2.46 % | 2.36 % | 1.26 % | 0.88 % | 0.81 % | 0.66 % | 0.60 % | 0.52 % | 0.50 % | 0.41 % |
| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 |
| 11.91 % | 8.89 % | 6.13 % | 2.65 % | 2.16 % | 2.03 % | 1.74 % | 1.34 % | 1.14 % | 0.99 % |
| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 |
| 10.45 % | 9.72 % | 4.98 % | 2.75 % | 2.47 % | 1.99 % | 1.69 % | 1.54 % | 1.06 % | 0.99 % |
Transparency adjustment sliders:
Transparency adjustment sliders:
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By clicking on a point in the plot you will be directly redirected to the corresponding position in the SNP Browser.
All GWAS calculations are based on SNPs called to the Morex v1 reference genome.
VCF Export of genotypic data
Germplasm details
Important hint: The following passport data reflects the state of data at the beginning of the project, which was also the basis for data analyses such as GWAS and genetic clustering. Passport data is mutable and can change due to the data curation of the responsible genebank during the course of the project or after the end of the project. Changes in the passport data that occurred afterwards are listed in the area one below with the title "Passport data changelog".
Saved germplasm collections
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