Assays
Assays is your own, private library of assays for which data was analyzed in Genotyper. The library is built up automatically by importing data in Genotyper.
In the Assays overview you can:
Adjust the assay Name by editing the text field. The assay Name will be used for your assay naming in the opened analysis view.
Set the ploidy level of the organism.
Adjust the allele X or Y label. These will be used in the Genotyper application and also in the export file, unless an export mapping is enabled for this assay.
The assay Reference is the unique identifier for each assay in Genotyper. This cannot be changed.
Flag an assay. Flagged assays will be visualized on top in the analysis matrix overview, when sorted on error messages 
. The flag is used for assays of which you know data clustering is not very clear and automated algorithm scoring will perform less, so manual review is always required.
Mark assays as absence/presence assays Clean up your assay list with the remove buttons. This is only an aid to visually clean up your assay list. If you upload data of a deleted assay, the history grids will still be available.
Import or export the assay list
Using the Actions menu in the right upper corner, you can:
Flag: bulk flag all assays/unflag all assays
Export/Import assays: If Genotyper does not get input for the assay alleles via the input files, they can be added to the assays with this feature. This is done by simply adjusting the export file and re-importing the csv.
Assay names are case-insensitive.The assay import can also be used to set export mappings or reference lines in bulk.
Be aware:
If you change your export mappings, this will also change in your exports. Even if you have allelenames configured. Exports are filled as follows:
If you have Export mappings configured, the export will use those, the user interface will still show Allelenames
If you have Allelenames but no Export Mappings configured, the export will use the combined Allelenames (so A:G for a heterozygote that has allelenames A & G), the user interface will also Show Allelenames
If you have no Allelenames or Export Mappings configured, the export will contain the default names (X:Y for a heterozygote)
Polyploid organisms
Genotyper supports the analysis of polyploid crops, by expanding the range of classes available for sample scoring.
By default each assay is diploid, and the ploidy level can be adjusted per assay.
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.
Assay detail settings
Click on a line item to open the assay.
General
When an assay is opened, the history grid of the assay can be viewed and edited. Results of all authorized data for this assay and reader combination is added to the history grid. The history grid is always saved per reader as readers can have small calibration differences. The number of PCR plates that is included in the history grid is visualized at the top of the graph.
Following options are available for each grid:
Lock: Each reader history can be locked individually for an assay. By doing this, no more data will be added to the history grid when an analysis is authorized.
Erase selection: This eraser can be used to clean up the history grid in case clusters are overlapping.
Clear: This button clears the entire history grid and resets the counter of the included PCR plates to 0.
Assay comments can be added to the assay record. Here you can add important information about an assay. A comment can be edited or deleted afterwards by the user who has written the comment. Assays with a comment are visualized with the comment icon 
in the assay results view.
Reference Lines
Genotyper supports the possibility to configure reference lines for your laboratory. A reference line is a plant of which the genotype calls are known to you in advance. Many laboratories add such controls to their experiments to verify their process efficiency and simplify manual result review. Samples defined as a Reference Line are visualized as a triangle in the color of their expected call.
A Failed control samples warning can be set in case the call for this reference doesn’t match the expected call. In the plate view the result is visualized with a checkmark in case the algorithm call matches the expected result, an ‘!’ in case the algorithm calls a different result than the expected call, or a ‘?’ if the reference line sample is uncalled.
Configuring controls
Read more about this topic here.
Export Mappings
In the assay details view you will find the ‘Export Mappings’ tab.
Here you can set a mapping for each genotype in the assay, which will be used in the export files.
If both an Allelename (set in Assay module) and export mapping are available, the Export Mapping will have priority to be used in the export file.
