Vidjil: A Web Platform for Analysis of ...
Document type :
Compte-rendu et recension critique d'ouvrage
Title :
Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing
Author(s) :
Duez, Marc [Auteur]
School of Social and Community Medicine [Bristol]
Site de Recherche Intégrée en Cancérologie [SIRIC-ONCOLille]
Giraud, Mathieu [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Herbert, Ryan [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Rocher, Tatiana [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Salson, Mikael [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Thonier, Florian [Auteur]
Institut Necker Enfants-Malades [INEM - UM 111 (UMR 8253 / U1151)]

School of Social and Community Medicine [Bristol]
Site de Recherche Intégrée en Cancérologie [SIRIC-ONCOLille]
Giraud, Mathieu [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Herbert, Ryan [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Rocher, Tatiana [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Salson, Mikael [Auteur]

Bioinformatics and Sequence Analysis [BONSAI]
Thonier, Florian [Auteur]
Institut Necker Enfants-Malades [INEM - UM 111 (UMR 8253 / U1151)]
Journal title :
PLOS ONE
Publisher :
Public Library of Science
Publication date :
2016-11-11
ISSN :
1932-6203
English keyword(s) :
Repertoire sequencing RepSeq
web-based application
computer software
lymphocytes
Acute lymphoblastic leukaemia
VDJ recombinations
web-based application
computer software
lymphocytes
Acute lymphoblastic leukaemia
VDJ recombinations
HAL domain(s) :
Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Algorithme et structure de données [cs.DS]
Informatique [cs]/Algorithme et structure de données [cs.DS]
English abstract : [en]
BackgroundThe 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 ...
Show more >BackgroundThe 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 ResultsVidjil 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.Show less >
Show more >BackgroundThe 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 ResultsVidjil 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.Show less >
Language :
Anglais
Popular science :
Non
Collections :
Source :
Files
- https://hal.archives-ouvertes.fr/hal-01397079/document
- Open access
- Access the document
- https://doi.org/10.1371/journal.pone.0166126
- Open access
- Access the document
- https://hal.archives-ouvertes.fr/hal-01397079/document
- Open access
- Access the document
- https://doi.org/10.1371/journal.pone.0166126
- Open access
- Access the document
- https://hal.archives-ouvertes.fr/hal-01397079/document
- Open access
- Access the document
- https://doi.org/10.1371/journal.pone.0166126
- Open access
- Access the document
- document
- Open access
- Access the document
- journal.pone.0166126.PDF
- Open access
- Access the document
- journal.pone.0166126
- Open access
- Access the document
- document
- Open access
- Access the document
- journal.pone.0166126.PDF
- Open access
- Access the document