Computational Analysis of B‐Cell Receptor (BCR) Immune Repertoires with Abalign

Abstract The widespread application of high‐throughput sequencing technology has generated massive sequences of B‐cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR‐specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high‐throughput processing capability. It offers ultra‐fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step‐by‐step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/ . © 2024 Wiley Periodicals LLC. Basic Protocol 1 : Resource preparation Basic Protocol 2 : Analyzing BCR immune repertoires Support Protocol 1 : Aiding antibody humanization Support Protocol 2 : Constructing B‐cell lineage trees Alternate Protocol : Running with Linux command line Basic Protocol 3 : Comparing BCR immune repertoires