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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data

View ORCID ProfileGuillaume Carissimo, View ORCID ProfileMarius van den Beek, Juliana Pegoraro, Kenneth D Vernick, View ORCID ProfileChristophe Antoniewski
doi: https://doi.org/10.1101/048983
Guillaume Carissimo
1Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris 75015, FRANCE
2CNRS, Unit of Hosts, Vectors and Pathogens (URA3012), Paris 75015, FRANCE
3Laboratory of Microbial Immunity, Singapore Immunology Network, A*STAR, 8A Biomedical Grove, Biopolis, Singapore 138648
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  • ORCID record for Guillaume Carissimo
Marius van den Beek
4Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), Developmental Biology Department, F-75005, Paris, France
5Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
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Juliana Pegoraro
4Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), Developmental Biology Department, F-75005, Paris, France
5Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
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Kenneth D Vernick
1Institut Pasteur, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris 75015, FRANCE
2CNRS, Unit of Hosts, Vectors and Pathogens (URA3012), Paris 75015, FRANCE
6Department of Microbiology, University of Minnesota, Minneapolis, MN 55108
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Christophe Antoniewski
4Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), Developmental Biology Department, F-75005, Paris, France
5Sorbonne Universités, Université Pierre et Marie Curie (UPMC), CNRS, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, F-75005, Paris, France
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  • For correspondence: christophe.antoniewski@upmc.fr
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Abstract

We present user-friendly and adaptable software to provide biologists, clinical researchers and possibly diagnostic clinicians with the ability to robustly detect and reconstruct viral genomes from complex deep sequence datasets. A set of modular bioinformatic tools and workflows was implemented as the Metavisitor package in the Galaxy framework. Using the graphical Galaxy workflow editor, users with minimal computational skills can use existing Metavisitor workflows or adapt them to suit specific needs by adding or modifying analysis modules. Metavisitor can be used on our Mississippi server, or can be installed on any Galaxy server instance and a pre-configured Metavisitor server image is provided. Metavisitor works with DNA, RNA or small RNA sequencing data over a range of read lengths and can use a combination of de novo and guided approaches to assemble genomes from sequencing reads. We show that the software has the potential for quick diagnosis as well as discovery of viruses from a vast array of organisms. Importantly, we provide here executable Metavisitor use cases, which increase the accessibility and transparency of the software, ultimately enabling biologists or clinicians to focus on biological or medical questions.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 20, 2016.
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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data
Guillaume Carissimo, Marius van den Beek, Juliana Pegoraro, Kenneth D Vernick, Christophe Antoniewski
bioRxiv 048983; doi: https://doi.org/10.1101/048983
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Metavisitor, a suite of Galaxy tools for simple and rapid detection and discovery of viruses in deep sequence data
Guillaume Carissimo, Marius van den Beek, Juliana Pegoraro, Kenneth D Vernick, Christophe Antoniewski
bioRxiv 048983; doi: https://doi.org/10.1101/048983

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