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Section: New Software and Platforms

Vidjil

High-Throughput Analysis of V(D)J Immune Repertoire

Keywords: Bioinformatics - NGS - Indexation - Cancer - Drug development

Scientific Description

Vidjil is made of three components: an algorithm, a visualisation 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 gather 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.

Functional Description

Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes. V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of a lymphoid population with dedicated Rep-Seq methods and software.

  • Participants: Mathieu Giraud, Mikaël Salson, Marc Duez, Ryan Herbert, Tatiana Rocher and Florian Thonier

  • Partners: CHRU Lille - CNRS - Inria - Université de Lille

  • Contact: Mathieu Giraud

  • URL: http://www.vidjil.org