Polyploid organisms
Genotyper now enables the analysis of polyploid crops, further enhancing your data interpretation capabilities:
Enhanced scoring: For polyploid analyses, an expanded range of classes becomes available for sample scoring
Ploidy management: Ploidy can be set and edited per assay within the assay module (default: diploid)
Configuration options: Reference lines and Export mappings can be configured for these classes directly on the assay details page.
Note on polyploid scoring: the AI currently only scores the three common classes (homozygous X, homozygous Y, heterozygous XY). Additional classes require manual scoring. For inquiries regarding automated polyploid data analysis beyond these initial capabilities, please contact your Breed Bio representative.
Continuous data upload
As part of the Breed Bio LIMS, we have developed the possibility to automate your lab flow by continuously uploading fluorescence datafiles. As soon as an output file is created by your fluorescence reader, this file can be added to the corresponding analysis in Genotyper. This enables near real-time scoring of your data.
If you are interested in, please reach out to your Breed Bio contact person for more details.
Passive reference dye
Genotyper's plate view now offers improved visualization for passive reference dye. As before, higher PRD values appear dark, while lower values appear lighter. Additionally, higher PRD values are now displayed as larger dots, while lower values are displayed as smaller dots.
Wells below the instrument's shortfall threshold are clearly marked with a white well and a blue exclamation mark for easy identification.
PRD values are also added to the sample table (available via the table icon 
in the right upper corner of the plate). This enables easy sorting to see the spread of PRD values across the entire plate.
Export settings
Configure your export file name
Navigate to Settings > Integration > Export filename pattern to discover a new setting to customize export filenames. The filename field can be composed by dragging and dropping variables into the filename pattern.
Note that for Intellics and Fluidigm exports, the input filename will be appended in order to diversify between multiple export files. Please reach out to your Breed Bio contact person for more details about this feature.
Configuration of Positive controls
Genotyper 3.3 offers improved options for discovering and configuring your positive controls. Please contact your Breed Bio representative for more details and to collaborate on finding the optimal configuration for your needs.
UI improvements to love
Assay and sample selection
A refreshed and more intuitive way to view your selected assays and samples.
Truncating settings
Truncating settings are improved under Settings > General > System settings. Use these to configure how your lab prefers to truncate long names for assays and PCR plates. PCR plates are now truncated in both matrix view and PCR Plate table.
User edits visualized
The familiar pencil icon, previously only in the plate table, now also appears on matrix view cards. This enhancement allows you to rapidly identify plates that contain manual edits.
Note for partial imports: when adding new assays or new plates, the pencil icon will stay in place. When adding new reads to the edited plate, the plate will be re-analyzed by the algorithm and the pencil icon disappears.
Grid lines
You can now visualize grid lines in the plot view. Use the shortkey 'g' to quickly show/hide them, or click the icon 
in the plot view. To set grid lines as enabled by default across all plots, navigate to Settings > General > Graph Settings and select 'show grid lines in graphs' for 'Graph grid lines'.
Keep sample selected after scoring
A new button is added to the plot view to keep samples selected after scoring. Note that this toggle should be enabled in each analysis individually.
