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) 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, 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 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 sequencing data, and view results. The 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, refer to Local Run Manager Software. |
| • | Universal Copy Service (UCS)—Copies sequencing and analysis data from the instrument to the output folder and uploads sequencing data to BaseSpace Sequence Hub (if applicable). |
Optional software used off-instrument includes the Sequencing Analysis Viewer (SAV). For more information, refer to Sequencing Analysis Viewer.
