There are two possibilities for new analyses to be imported in Genotyper: uploading files or using our Kraken LIMS integration.
File based import
To import files, click on Create new in the upper right corner of the Analysis Overview. You can then drag and drop one or more files or click on the Upload new files button to open the file explorer.
Upload multiple files to to group them in one analysis
Upload multiple files one by one to organize one file per analysis
Uploaded files can be deleted via the 
button.
For Nexar/ Arraya or Intelliqube files (arraytape), the instrument must be selected if multiple arraytape-supporting instruments are available in your laboratory environment.
Click Analyze to start the analysis.
Note: When a file is uploaded that was already analyzed in the past, a warning is shown that that file was already analyzed with a link to the previous analysis.
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.
Kraken integration
Kraken projects can be imported and analyzed automatically. This will be possible after installation and configuration of the Kraken app.
Automated import
In this mode, Kraken is continuously monitored for projects in a particular status. When a project is changed to this status, the project is automatically imported into Genotyper.
Manual import
If automated import is not the preferred way of working, it is possible to manually select the Kraken project for import. Click the Import kraken analysis button in the upper right corner, fill in the Kraken customer and project number, separated with a ‘.’ and confirm with Import.
A message will confirm the command was sent successfully to Kraken. The message will disappear automatically and as soon as the analysis is created each analysis will appear as a unique analysis in the overview table.
Kraken app status indicators
Kraken app status indicators
The Kraken data will only be imported if the Kraken app is connected. The connection status is indicated in green or red, next to the Kraken import button.
Analysis status
Each analysis that is imported into Genotyper will have a status that informs you about the progress of the analysis. The analyses are organized in 4 tabs, depending on their status: Open, Authorized, Discarded or All.
All available statuses
All available statuses
Creating: a new, empty, analysis is being created
Importing: the data is being imported into the analysis
Imported: the data is imported
Import failed: the import has failed. Navigate to the Audit logs module for more information.
Analysis pending: waiting to be analyzed
Analyzing: algorithm is currently analyzing the data
Analyzed: the algorithm is finished analyzing the data
Analysis failed: the algorithm failed to analyzed the data
Exported: an export has been created for this analysis. If this is a Kraken order, the data is also sent to Kraken. Results can still be edited. This status is optional and can be skipped by authorizing an analysis with status analyzed.
Authorized: Results can no longer be edited. This means the analysis has been used to update the history grids. If applicable, a new export is created (and data is exported to Kraken).
Discarded: Via the actions-button, you can choose to discard an analysis to keep the overview table clean. Authorized analysis cannot be discarded and discarded data cannot be viewed anymore. Upon discarding, you are enforced to add a reason which can be traced back in the audit log module as a discard log type. Note that discarding an analysis does not impact the analyzed datapoints counter in the Usage module, where each analyzed datapoint is counted.
You can search the analyses overview table by using filters.
The settings wheel 
gives the possibility to configure the table by moving, showing and hiding columns. Column settings and filters are saved in your own browser session.
Opening an analysis
Click a row in the table to open the analysis. To open the analysis in a new tab, use Ctrl + Click (Mac: Cmd + Click).
Add new file(s)
Adding new data to an existing analysis can be performed multiple times as long as the analysis is not authorized. Genotyper searches for differences between the original analysis and newly imported data, and only newly discovered plates, assays and reads (fluorescence) are then added.
Read more about this topic here.