Paired Clonotype Diversity is a metric used to evaluate clonotype diversity in single-cell V(D)J sequencing data. It calculates the number of clonotypes in the same cell based on paired heavy and light chain V(D)J rearrangement information, clustering different clonotypes across cells, and determining the average number of clonotypes in each cluster. This metric is typically used to describe the clonotype diversity within individual cells.

The specific calculation process for Paired Clonotype Diversity is as follows:

1. Concatenate the heavy and light chain V(D)J sequences in eachcell to obtain a full-length V(D)J sequence.

2. Use V(D)J analysis software to analyze the full-length V(D)Jsequences and obtain clonotype information for the same cell.

3. Cluster the clonotypes within the same cell and calculate thenumber of clonotypes in different clusters.

4. Calculate the inverse Simpson index of the number of cells perclonotype to obtain the Paired Clonotype Diversity metric.

A higher Paired Clonotype Diversity value indicates greater clonotype diversity within single cells, meaning that more distinct clonotypes are present in individual cells. This metric can be used to compare the effects of different cell types, experimental conditions, and treatments on clonotype diversity within single cells. It's worth noting that Paired Clonotype Diversity reflects clonotype diversity within the sample. The Paired Clonotype Diversity value is included in the VDJ annotation section of MobiVision's websummary.html quality control results, providing a reference for clonotype diversity.