Can secondary analysis run on MiSeq while a run is in progress?

It is not possible to perform secondary analysis on the MiSeq when a sequencing run is in progress.

If a new sequencing run is started on the MiSeq before the secondary analysis of a previous run is complete, the secondary analysis is stopped automatically.

MiSeq computing resources are dedicated to either sequencing or analysis, and the system is designed in such a way that a sequencing command overrides an analysis command.

Secondary analysis can later be requeued from the MiSeq Reporter or Local Run Manager Analyses tab, when sequencing is not in progress.

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