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PLoS One. 2016 Nov 11;11(11):e0166126. doi: 10.1371/journal.pone.0166126. eCollection 2016.

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

Author information

1
School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.
2
SIRIC ONCOLille, 59000 Lille, France.
3
Université de Lille, CNRS, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, 59000 Lille, France.
4
Inria Lille, 59650 Villeneuve d'Ascq, France.
5
Inserm UMR1151, Institut Necker-Enfants Malades, Paris Descartes University and Necker–Enfants Malades Hospital–Paris, France.

Abstract

BACKGROUND:

The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.

METHODS AND RESULTS:

Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

PMID:
27835690
PMCID:
PMC5106020
DOI:
10.1371/journal.pone.0166126
[Indexed for MEDLINE]
Free PMC Article

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