System Software - illumina MiSeq System Manual

MiSeq System Guide
For more information on analysis workflows and manifest file formats, see the Local Run Manager Software
Guide (document # 1000000002702) .
For more information on sample sheets, see the MiSeq Sample Sheet Quick Reference Guide (document #
15028392) .

System Software

The instrument software suite includes integrated applications that perform sequencing runs, on-instrument
analysis, and related functions.
MiSeq Control Software (MCS)—Controls instrument operation. The MiSeq Control Software (MCS)
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interface guides you through the steps to load the flow cell and reagents before beginning the run. An
overview of quality statistics appears as the run progresses.
During the run, MCS operates the flow cell stage, dispenses reagents, controls flow cell temperatures,
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and captures images of clusters on the flow cell. MCS performs the run according to parameters
specified in the Local Run Manager software.
Real-time analysis (RTA) software—Performs image analysis and base calling, and assigns a quality score
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to each base for each cycle. Images are temporarily stored in the run folder for processing by RTA, and
then automatically deleted when analysis by RTA is complete.
Local Run Manager—An on-instrument integrated solution used to create a run, monitor status, analyze
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sequencing data, and view results. Local Run Manager also tracks sample information and controls user
permissions. The software runs as a Windows service on the instrument computer and is viewed through
a web browser. For more information see
Optional software used off-instrument includes the Sequencing Analysis Viewer (SAV). For more information,
see Sequencing Analysis Viewer on page
Status Icons
A status icon on the control software interface indicates a change in conditions during run setup or during the
run. A number on the icon indicates the number of conditions for a status.
When a run status changes, the icon blinks to alert you. Select the icon to view a description of the condition.
Select Acknowledge to clear the message, and then Close to close the dialog box.
Filter the types of messages that appear in the status window by selecting the icons along the top margin of
the window. Selecting an icon toggles the condition to show or hide.
Status Status Description
Icon Name
Status No change. System is normal.
OK
Attention Important information. Action is recommended.
Warning Warnings do not stop a run. However, some warnings require action before proceeding.
Error Errors usually stop a run and generally require action before proceeding with the run.
Document # 15027617 v04 Material # 20024228
For Research Use Only. Not for use in diagnostic procedures.
Local Run Manager Software on page
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