Rarefaction for Clonotypes
The rarefaction curve (
) is also known as the species accumulation curve (figure 7.22). It shows the expected number of distinct clonotypes discovered as a function of the total number of detected clonotypes, together with the confidence interval (CI), obtained from a normal approximation. The curve is
- interpolated down to 0 clonotypes;
- extrapolated to twice the total number of detected clonotypes.
When only a few clonotypes have been detected, there is a high probability that the next read will represent a new clonotype, causing the curve to rise steeply. As more clonotypes are detected, it becomes increasingly likely that subsequent reads represent clonotypes already observed, so the curve gradually flattens
Figure 7.22: Rarefaction plot for the TRA chain. The chain can be changed from the side panel.