Section: New Software and Platforms
Vidjil – Quantifying lymphocyte rearrangements in high-throughput sequencing data
Software web site: http://bioinfo.lille.inria.fr/vidjil/
Objective: Vidjil is a platform for high-throughput V(D)J recombinations analysis. containing three components. The Vidjil algorithm process high-througput sequencing data to extract V(D)J junctions and gather them into clones. Vidjil starts from a set of reads and detects “windows” overlapping the actual CDR3. This is based on an fast and reliable seed-based heuristic and allows to output all sequenced clones. The analysis is extremely fast because, in the first phase, no alignment is performed with database germline sequences  . The Vidjil dynamic browser is made for the visualization and analysis of clones and their tracking along the time in a “minimal residual disease” setup or in a immunological study. The browser visualize data processed by the Vidjil algorithm or by other V(D)J analysis pipeline and enables to explore further cluterings. Finally, a patient database with a server links the browser and the algorithmic part. The goal is that the clinicians will be able to upload, manage and process their runs on a server hosted in their hospital.
In 2014, the development of Vidjil was supported by the SIRIC OncoLille (Marc Duez). We developed the new patient database and added features both on the browser and on the algorithm (multi-system analysis). Several hospital labs in France and in Europe are testing Vidjil. The Lille hospital plans to use Vidjil in 2015 in a pre-production pipeline.