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Wednesday, June 29 • 2:20pm - 2:40pm
Metavisitor, a suite of Galaxy tools and workflows for detection or discovery of viruses in NGS datasets

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Slides    doi:10.7490/f1000research.1112468.1

Authors

Marius van den Beek, Institut de Biologie Paris Seine
Guillaume Carissimo, Institut Pasteur; Juliana Pegoraro, Institut de Biologie Paris Seine
Kenneth D Vernick, Institut Pasteur; and Christophe Antoniewski, Institut de Biologie Paris Seine

Abstract
In the aim of providing biologists and medical doctors with an accessible and adaptable software to detect and reconstruct viral genomes from sequencing datasets, we implemented in Galaxy a set of tools and workflows called Metavisitor. This suite of tools and workflows can be used directly upon access to our Mississippi server or installed on any Galaxy server instance. Using the graphical Galaxy workflow editor, the Metavisitor workflows can be adapted to suit specific needs, by adding analysis steps or replacing/modifying existing ones. Metavisitor works with DNA, RNA or small RNA sequencing data that provide different read lengths and can use combination of a de novo and guided approaches to assemble viral genomes from sequencing reads. Thus, the software has the potential for quick diagnosis as well as discovery of viruses (or other pathogens) from a vast array of organisms. Importantly, we are working at an executable paper on how to use Metavisitor in various use-cases as well as at an ansible-based procedure to easily deploy a Metavisitor Galaxy instance on available hardware. We hope that these development lines will increase the accessibility and transparency of Metavisitor and help researchers to focus on biological or medical issues.

Speakers
avatar for Christophe Antoniewski

Christophe Antoniewski

Head of ARTbio bioinformatics, CNRS - Institut de Biologie Paris Seine
avatar for Marius van den Beek

Marius van den Beek

IBPS / Université Pierre et Marie Curie



Attendees (18)