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3 Publications visible to you, out of a total of 3
vadr database of Porcine CircoVirus (handle PCV 1, 2, 3 and 4 complete genomes available the 2023/07/12 YYYY/MM/DD on NCBI nt db, computed with vadr 1.6.4)

Abstract (Expand)

vadr database of Porcine CircoVirus (handle PCV 1, 2, 3 and 4 complete genomes available the 2024/04/02 YYYY/MM/DD on NCBI nt db, computed with vadr 1.6.4) vadr is an annotation program for viruses, …, based on models computed on known viruses this database can be used for example to analyse pcv variants using vadr and vardict-java results by using vvv2_display tool.  

Author: Fabrice Touzain

Date Published: 2025

Publication Type: Dataset

vvv2_align_SE, vvv2_align_PE/vvv2_display: Galaxy-Based Workflows and Tool Designed to Perform, Summarize and Visualize Variant Calling and Annotation in Viral Genome Assemblies

Abstract (Expand)

Background: Next-generation sequencing (NGS) analysis of viral samples generates results dispersed across multiple files—genome assembly, variant calling, and functional annotations—making integrated … interpretation challenging. Variants often yield numerous low-frequency or non-significant variants, yet only a small fraction are biologically relevant. Virologists must manually sift through extensive data to identify meaningful mutations, a time-consuming and error-prone process. To address these practical challenges, we developed vvv2_display, a dedicated summarization and visualization tool, integrated within comprehensive Galaxy workflows. Results: vvv2_display streamlines variant interpretation by consolidating key results into two concise and interoperable outputs. The first output is a PNG image showing alignment coverage depth and genomic annotations, with significant variants displayed along the genome as symbols whose height reflects frequency and shape indicates the affected protein. At a glance, this enables virologists to identify all deviations from a reference viral genome. Each significant variant is assigned a unique identifier that directly links to the second output: a tab-separated (TSV) text file listing only high-confidence variants, with frequencies, flanking nucleotides, and impacted genes and proteins. This cross-referenced design supports rapid, accurate, and intuitive data exploration. Availability: vvv2_display is open source, available on Github and installable via Mamba.

Authors: Alexandre Flageul, Edouard Hirchaud, Céline Courtillon, Flora Carnet, Paul Brown, Béatrice Grasland, Fabrice Touzain

Date Published: 17th Oct 2025

Publication Type: Journal Article

vvv2_display: variant calling pipeline summarized in two outputs, png image of variants (proportion, annotation and coverage depth), tsv file of significant variants information

Abstract

Explain vvv2_display command line program and its inputs/outputs, available as a bioinconda package. Describes workflows using this program in Galaxy.

Authors: Alexandre Flageul, Edouard Hirchaud, Céline Courtillon, Flora Carnet, Paul Brown, Béatrice Grasland, Fabrice Touzain

Date Published: 2025

Publication Type: Other

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