Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire
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README.org

README.org

Vidjil – High-throughput Analysis of V(D)J Immune Repertoire

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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. 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 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.

Vidjil components

The algorithm

The web application

Code and license

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://git.vidjil.org/. Bug reports, issues and patches are welcome.

The Vidjil team

Vidjil is developed by Mathieu Giraud, Ryan Herbert, Tatiana Rocher and Mikaël Salson from the Bonsai bioinformatics team (CRIStAL, CNRS, U. Lille, Inria Lille). Vidjil is also developed by external colleagues: Marc Duez located in Bristol (School of Social and Community Medicine, University of Bristol) and Florian Thonier located in Paris (department of hematology, Necker hospital) Vidjil is developed in collaboration with the department of Hematology of CHRU Lille, the Functional and Structural Genomic Platform (U. Lille 2, IFR-114, IRCL), and the EuroClonality-NGS working group. The research is supported by SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), by Région Nord-Pas-de-Calais (ABILES) and by Inria.

References

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

Marc Duez et al., “Vidjil: High-throughput analysis of immune repertoire”, submitted

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

You may also be interested in the following publication for the diagnosis of acute lymphoblastic leukemia with high-throughput sequencing:

Yann Ferret, Aurélie Caillault, et al., “Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis”, British Journal of Haematology 2016 http://dx.doi.org/10.1111/bjh.13981