Sequencing

To perform a sequencing run on the MiSeq, follow the setup steps described in this section.

There are three options in MiSeq Control Software (MCS) for configuring the run setup:

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Local Run Manager— Select a run that has been prepared with the Local Run Manager.

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Sample Sheet—Create a run using sample sheets. Sample sheets are validated in Local Run Manager.

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Manual—Create a run by manually entering run information. No on-board secondary analysis is performed when this option is selected.

After the run begins, no other user intervention is required.

Use one of the following approaches to monitor the sequencing run:

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BaseSpace Sequence Hub— Access the run status through this platform.

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Instrument Interface— Use the sequencing screen on the instrument itself.

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Remote Monitoring with Sequencing Analysis Viewer (SAV)— Download and use the SAV as an optional application accessible via the Illumina website.

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Remote Monitoring with Local Run Manager— Observe the run on the instrument or remotely using Local Run Manager.

After the sequencing run is complete, perform an instrument wash.