ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intra-clonal diversities: application to human B-cell tumors

High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound Ig part of the BCR). AIRR-seq data allows researchers to examine intra-clonal differences caused primarily by somatic hypermutations and affinity maturation. Exploring the diversity of antibodies and understating how they evolve could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Consequently, retracing their evolutionary history could also help to clarify how vaccines or pathogen exposition drive the humoral immune response. Computational methods are necessary for large-scale evaluation of AIRR-seq properties. Currently, there is no efficient and interactive tool for analyzing intra-clonal diversity, permitting users to explore AIRR-seq data and potentially discover discriminating clonal features. We developed ViCloD, a web server for large-scale visual analysis of repertoire clonality and intra-clonal diversity. ViCloD uses data preprocessed by IMGT and performs evolutionary and statistical analyses, producing a set of plots. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intra-clonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as image files. ViCloD is a versatile analytical tool that can help researchers and clinicians in their studies involving B cell clonal diversity. It is user-friendly, simple, accessible, and open to all users. Moreover, its pipeline is optimized to process hundreds of thousands of sequences in a few minutes, allowing intra-clonal diversity analysis in large and complex repertoires. Availability and implementation The web server is available at http://www.lcqb.upmc.fr/viclod/. The pipeline is available at github and allows users to run analyses locally.