CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants

BMC Bioinformatics, vol. 25, pp. 376

Abstract

BACKGROUND: Methods to call, analyze and visualize copy number variations (CNVs) from massive parallel sequencing data have been widely adopted in clinical practice and genetic research. To enable a streamlined analysis of CNV data, comprehensive annotations and good visualizations are indispensable. The ability to detect single exon CNVs is another important feature for genetic testing. Nonetheless, most available open-source tools come with limitations in at least one of these areas. One additional drawback is that available tools deliver data in an unstructured and static format which requires subsequent visualization and formatting efforts. RESULTS: Here we present CNVizard, an interactive Streamlit app allowing a comprehensive visualization of CNVkit data. Furthermore, combining CNVizard with the CNVand pipeline allows the annotation and visualization of CNV or SV VCF files from any CNV caller. CONCLUSION: CNVizard, in combination with CNVand, enables the comprehensive and streamlined analysis of short- and long-read sequencing data and provide an intuitive webapp-like experience enabling an interactive visualization of CNV data.

Authors 9

1. Jeremias Krause corresponding Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany. jerkrause@ukaachen.de

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

2. Carlos Classen Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

3. Daniela Dey Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

4. Eva Lausberg Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

5. Luise Kessler Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

6. Thomas Eggermann Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

7. Ingo Kurth Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

8. Matthias Begemann Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany

9. Florian Kraft Aachen Medical Faculty Institute for Human Genetics and Genomic Medicine

   Universitätsklinikum Aachen · RWTH Aachen University

   Affiliation as printed

   Medical Faculty, Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, North-Rhine-Westphalia, Germany