Our objectives were as follows: (1) to develop a reliable 5’ RACE protocol for generating NGS libraries for evaluating populations of canine B cells, (2) to develop an open-source bioinformatics pipeline for processing canine antigen receptor sequencing data, and (3) to apply these sequencing and bioinformatics methods to derive insights into the BCR repertoires of healthy dogs and dogs undergoing treatment for intermediate-to-large B-cell lymphoma, a common canine hematopoietic neoplasm that we used as a model for B-cell clonality. Here, BCR is linked to hematopoietic and lymphoid cell neoplasm.