Vidjil analyses high-throughput sequencing data from lymphocytes. Vidjil is used for characterizing lymphocyte populations and is especially used in the context of blood cancers. Vidjil is made of three components: an algorithm, a visualization browser and a server that allow an analysis of lymphocyte populations containing V(D)J recombinations. Vidjil high-throughput algorithm extracts V(D)J junctions and gathers them into clones. This analysis is based on a spaced seed heuristics and is fast and scalable, as, in the first phase, no alignment is performed with database germline sequences. Each sequence is put in a cluster depending on its V(D)J junction. Then a representative sequence of each cluster is computed in time linear in the size of the cluster. Finally, we perform a full alignment using dynamic programming of that representative sequence against the germline sequences. Vidjil also contains a dynamic browser (with D3JS) for visualization and analysis of clones and their tracking along the time in a MRD setup or in an immunological study.