Introduction
MiSeq sequencing data can be analyzed on the instrument computer using MiSeq Reporter or on the cloud using BaseSpace. Both MiSeq Reporter and BaseSpace produce information about alignment, structural variants, and/or contig assemblies for each genome requested and each sample (if a run is multi-sample). In addition, BaseSpace provides a mechanism to share data with others and easily scale storage and computing needs.
When setting up runs on the MiSeq, you have the option to send the run to BaseSpace. This will send the base call *.BCL files to your dedicated space on the cloud, as well as associated files, like the sample sheet. BaseSpace supports the same analysis jobs for post-base-calling analysis as the MiSeq Reporter.
You can reach BaseSpace from the MiSeq instrument computer, or through BaseSpace.illumina.com. Use your Illumina account to log on; the first time you visit you will be asked to accept the BaseSpace agreement. After that, you are ready to run your analysis on BaseSpace.
Figure 1 BaseSpace Analysis Option for MiSeq Data
BaseSpace Data Model
The BaseSpace data model revolves around runs and projects:
• Sequencing runs are automatically uploaded from the sequencing instrument to BaseSpace as they become available. The runs consist of one or more samples. You can monitor these runs and check data quality of the samples before continuing analysis.
• Projects consist of samples, derived from one or more of the runs, as determined by the sample sheet. Within the projects, you can run apps on the samples to perform an analysis. The app results provide access to the analysis metrics and output files. Figure 2 BaseSpace Data Model
