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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 softwares.

The Vidjil platform contains three components. Vidjil-algo processes high-througput sequencing data to extract V(D)J junctions and gather them into clones. Vidjil-algo 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 web application is made for the interactive visualization and analysis of clones and their tracking along the time in a MRD setup or in a immunological study. The web application can visualize data processed by the Vidjil algorithm or by other V(D)J analysis pipelines, and enables to explore further cluterings proposed by software and/or done manually done by the user. The web application can be linked to a sample, experiment and patient database able to store sequencing data and metadata, to run RepSeq software and to save annotations directly from the web application, with authentication. Clinicians or researchers in immunology or hematology can manage, upload, analyze and annotate their runs directly on the web applicaiton.

• Stable releases can be downloaded from http://bioinfo.lille.inria.fr/vidjil and http://www.vidjil.org/releases
• Development code is under algo/
• Documentation, compilation and installation instructions: doc/vidjil-algo.md

• Public test server at https://app.vidjil.org/ (demo login: [email protected], password: vidjil)
• Please contact us if you would like to test your data and have a full account on the web server
• We offer hosting solutions for healthcare compliance
• Development code is under browser/ and server/ (a make in those directories will get the necessary files)
• Documentation is in doc/, it is also available from http://www.vidjil.org/doc

Vidjil is open-source, released under GNU GPLv3 license. You are welcome to redistribute it under certain conditions. This software is for research use only and comes with no warranty.

The development code is available on http://gitlab.vidjil.org/. Bug reports, issues and patches are welcome.

We welcome Bitcoin donations to 13u12m6LxVhesKEpS6T5wpYN19LHpwk8xt. Thank you for your support !

Vidjil is developed and maintained by the Bonsai bioinformatics lab at CRIStAL (UMR CNRS 9189, Université Lille) and the VidjilNet consortium at Inria. See doc/credits.md for the full list of contributors, collaborators, and funders.

Contact: Marc Duez, Florian Thonier, Mathieu Giraud and Mikaël Salson.

If you use Vidjil for your research, please cite the following references:

Marc Duez et al., “Vidjil: A web platform for analysis of high-throughput repertoire sequencing”, PLOS ONE 2016, 11(11):e0166126 http://dx.doi.org/10.1371/journal.pone.0166126

Mathieu Giraud, Mikaël Salson, et al., “Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing”, BMC Genomics 2014, 15:409 http://dx.doi.org/10.1186/1471-2164-15-409

The Vidjil platform has been utilised in 35+ publications in oncology, hematology, and immunology.