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

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.
Type de document :
Article dans une revue
PLoS ONE, Public Library of Science, 2016, 11 (11), 〈10.1371/journal.pone.0166126〉
Liste complète des métadonnées

Littérature citée [12 références]  Voir  Masquer  Télécharger

https://hal.archives-ouvertes.fr/hal-01397079
Contributeur : Mikaël Salson <>
Soumis le : mardi 15 novembre 2016 - 14:12:45
Dernière modification le : vendredi 22 mars 2019 - 01:33:42
Document(s) archivé(s) le : jeudi 16 mars 2017 - 18:22:49

Fichier

journal.pone.0166126.PDF
Fichiers éditeurs autorisés sur une archive ouverte

Identifiants

Citation

Marc Duez, Mathieu Giraud, Ryan Herbert, Tatiana Rocher, Mikael Salson, et al.. Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing. PLoS ONE, Public Library of Science, 2016, 11 (11), 〈10.1371/journal.pone.0166126〉. 〈hal-01397079〉

Partager

Métriques

Consultations de la notice

1075

Téléchargements de fichiers

166