The EPI2ME desktop agent can be started as soon as basecalled data (in fastq or fastq.gz format) becomes available.

Data acquisition through MinKNOW is performed independently of EPI2ME, thus EPI2ME can be run in parallel to MinKNOW facilitating real-time data analysis of acquired basecalled data.

Please note that if compute resource is limited, MinKNOW performance may be affected and data acquisition interrupted when other programs are running at the same time.

As EPI2ME takes fastq and fastq.gz files as input, the EPI2ME analysis workflows can also be started after sequencing and basecalling has been completed and fastq or fastq.gz files generated.

Users can provide an input folder of those files to perform analysis.