After the sequencing platform generates the sequencing images, the data are analyzed as following:

1. Image analysis — Uses the raw images to locate clusters, and outputs the cluster intensity, X,Y positions, and an estimate of the noise for each cluster. The
output from image analysis provides the input for base calling. Image analysis is performed by the instrument control software from Illumina.

2 Base calling — Uses cluster intensities and noise estimates to output the sequence of bases read from each cluster, a confidence level for each base, and whether the read passes filtering. Base calling is performed by the instrument control software’s Real Time Analysis (RTA) from Illumina.