Now your sequencing run is started, it is a good time to get EPI2ME running in the background. This allows reads to be sent into the workflow as soon as they have been acquired and basecalled.

If you have closed the EPI2ME Agent from earlier, please reopen it:

Click New analysis and select FASTQ control experiment.

If prompted, select a folder containing FASTQ files to be analysed. If a MinKNOW-generated folder structure is detected in the default input location, this will be shown in the Experiments & samples tab. You can change the default input location in the Settings page (cog icon) under Data sources.

Alternatively, you will be directed to the Folders tab, where you can select your input folder.

Adjust the run-time parameters of your analysis:
Select No under "Are you uploading human DNA/RNA?". Leave all the other settings at their default values, then click Accept & Start.

EPI2ME will start the workflow.