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

• Published in: PloS one Vol. 11; no. 11; p. e0166126
• Main Authors: Duez, Marc, Giraud, Mathieu, Herbert, Ryan, Rocher, Tatiana, Salson, Mikaël, Thonier, Florian
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 11.11.2016; Public Library of Science (PLoS)
• Subjects: Adaptive immunity; Algorithms; Base Sequence; Bioinformatics; Biology and Life Sciences; Blood cells; Computational Biology - methods; Computer and Information Sciences; Computer Science; Data processing; Data Structures and Algorithms; Deoxyribonucleic acid; DNA; DNA sequencing; Gene sequencing; Hematology; High-Throughput Nucleotide Sequencing - methods; Humans; Immune response; Immune system; Immunity; Immunoglobulins; Immunology; Internet; Internet software; Leukemia; Leukocytes; Lymphocytes; Lymphocytes - immunology; Lymphocytes - metabolism; Lymphocytes B; Lymphocytes T; Medical research; Medicine and Health Sciences; Nucleotide sequence; Physical sciences; Reproducibility of Results; Research and analysis methods; Sequence Homology, Nucleic Acid; Servers; Source code; T cell receptors; T cells; Therapeutic applications; V(D)J Recombination - genetics; Web Browser; computer software; lymphocytes; Acute lymphoblastic leukaemia; Repertoire sequencing RepSeq; web-based application; VDJ recombinations
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0166126

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. 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.