BCR CDR H3 sequence clustering.
To classify and cluster biologically similar BCRs that possess specificities similar to those of an antigen as single entities for downstream analysis, we retrieved individual clonotype information using VDJtools followed by clustering using a BCR clustering iteration method. The Hamming distance of all CDR H3 sequences was calculated in a matrix. A randomly selected BCR was allocated a cluster number of 1, acting as a “seed” sequence. Any sequences within 1 Hamming distance of this “seed” sequence was allocated the same cluster number, forming the second layer of sequences. These sequences at the second layer acted as additional “seed” sequences, whereby additional sequences within 1 Hamming distance were assigned to the same cluster. All CDR H3 sequences were allocated a cluster number through iteration of this process. With different clustering runs, different cluster numbers may have been assigned to the same cluster because of random cluster number allocation. Visualization of cluster networks was performed using the iGraph R package (