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Technical Note

PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data

1
Unit of Discovery and Molecular Characterization of Pathogens, Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
2
Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
3
Unité Environnement et Risque Infectieux, Institut Pasteur, Cellule d’Intervention Biologique d’Urgence, 75015 Paris, France
*
Authors to whom correspondence should be addressed.
Academic Editors: Franziska Hufsky, Alba Pérez-Cataluña, Walter Randazzo, Gloria Sanchez, Fernando González-Candelas and Manja Marz
Viruses 2022, 14(6), 1260; https://doi.org/10.3390/v14061260
Received: 29 April 2022 / Revised: 31 May 2022 / Accepted: 3 June 2022 / Published: 10 June 2022
(This article belongs to the Special Issue Virus Bioinformatics 2022)
The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and time-consuming task. As a result, we developed PIMGAVir and Vir-MinION, two metagenomics pipelines that automatically provide the user with a complete baseline analysis. The PIMGAVir and Vir-MinION pipelines work on 2nd and 3rd generation data, respectively, and provide the user with a taxonomic classification of the reads through three strategies: assembly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehensive results in graphical and textual format for future analyses. Finally, the pipelines equip the user with a stand-alone platform with dedicated and various viral databases, which is a requirement for working in field conditions without internet connection. View Full-Text
Keywords: taxonomic classification; metagenomic pipeline; 2nd and 3rd sequencing generation; multiple strategies analysis taxonomic classification; metagenomic pipeline; 2nd and 3rd sequencing generation; multiple strategies analysis
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MDPI and ACS Style

Mastriani, E.; Bienes, K.M.; Wong, G.; Berthet, N. PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data. Viruses 2022, 14, 1260. https://doi.org/10.3390/v14061260

AMA Style

Mastriani E, Bienes KM, Wong G, Berthet N. PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data. Viruses. 2022; 14(6):1260. https://doi.org/10.3390/v14061260

Chicago/Turabian Style

Mastriani, Emilio, Kathrina Mae Bienes, Gary Wong, and Nicolas Berthet. 2022. "PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data" Viruses 14, no. 6: 1260. https://doi.org/10.3390/v14061260

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