Workflow
When the investigator starts the sample preparation in the lab, until the information is displayed on the iSkyLIMS the run is going through several steps.
The following picture shows a summary of these steps for a NextSeq run.
During this phase the investigator is responsible to prepare the samples, the used library kits.
Investigator has to prepare the sample sheet that will be used later on for the wetlab Manager to create the run in iSkyLIMS.
The safest way to prepare the file is using the illumina software (IEM). With this tool the investigator will select the library kit used in his experiment and in will assign the indexes for each cell.
Check the Investigator role for more information about this file.
When saving the sample sheet file the investigator will delivery it to the wetlab Manager
This is the first action for wetlab Manager. He will open iSkyLIMS and selecting the Run Preparation option from the menu, he will upload the Sample Sheet created by the investigator.
After the run is created in iSkyLIMS, the wetlab Manager has to download the run file that will be used to create the run in illumina BaseSpace.
When the Amplification process ends in the sequencer, it will send all output files towards to external storage.
iSkyLIMS is checking a regularly bases if there are new run folders on the external storage server. When one is detected it will start the process to get some of them to fetch the necessary information and store the processed data into database.
The following picture shows a summary of these steps for a MiSeq run.
As you can see less steps are needed for a MiSeq run. This is because this sequencer create by itself, then it not requires any action from Investigator for this.
Once the Investigator prepare the samples an start the process in illumina MiSeq sequencer, all the steps will be done automatically.