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MiSeq System Guide
Sequencing During Analysis
The MiSeq system computing resources are dedicated to either sequencing or analysis.
With Local Run Manager, if a new sequencing run is started on the MiSeq before secondary analysis of an
earlier run is complete, a confirmation dialog box appears. After confirming you want the new sequencing run
to start, secondary analysis of the earlier run is stopped until the new run completes sequencing.
After the new run completes sequencing, secondary analysis of the earlier run automatically starts again from
the beginning.
Sequencing Analysis Viewer
You can monitor your run in greater detail without interfering with the run using the Illumina Sequencing
Analysis Viewer (SAV). Your MiSeq must be networked to view primary analysis results with SAV.
SAV allows you to review metrics during a run as metrics are generated, and later after a run has completed.
Install SAV onto a computer independent of the MiSeq with access to the same network connected to the
instrument. After launching the software, browse to the output folder for your run.
After template generation, SAV provides metrics generated by RTA and organizes the metrics into plots,
graphs, and tables.
NOTE
SAV is universal to Illumina sequencing systems, most of which use an 8-lane flow cell. Some views include
drop-down lists showing lanes 1–8. Because the MiSeq flow cell has a single lane, select All or Lane 1. For
more information, see the Sequencing Analysis Viewer User Guide (document # 15020619) .
Required Disk Space
The integrated instrument computer has approximately 550 GB of storage capacity.
Before starting a run, the software checks available disk space. If there is not enough disk space for the run,
a message indicating how much disk space is required appears.
If prompted to make disk space available, move or delete older run folders as appropriate. For more
information, see
Manage Files on page
MiSeq Reagent Kit Overview
The MiSeq Reagent Kit is a single-use reagent kit required to perform a sequencing run. It is available in
different types and sizes. Each type of MiSeq Reagent Kit includes a kit-specific flow cell type and all
reagents required for performing a run.
The flow cell, PR2 bottle, and reagent cartridge provided in the kit use radio-frequency identification (RFID)
for accurate consumable tracking and compatibility.
Always use the reagent cartridge associated with your flow cell type. If the reagent cartridge is not
compatible, a message appears during run setup that prompts you to load a compatible reagent cartridge.
For a description of available reagent kits, visit the
Flow Cell
The MiSeq flow cell is a single-use glass-based substrate where clusters are generated and the sequencing
reaction is performed.
Document # 15027617 v04 Material # 20024228
For Research Use Only. Not for use in diagnostic procedures.
38. After clearing adequate disk space, select Restart Check.
MiSeq Reagent Kits product page
on the Illumina website.
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