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© Pierre Gounon
Virus influenza purifié, agent de la grippe. Ce virus enveloppé possède un génome fragmenté : 8 segments d'ARN négatif protégés par une nucléocapside.
Publication : Viruses

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Viruses - 10 Jun 2022

Mastriani E, Bienes KM, Wong G, Berthet N,

Link to Pubmed [PMID] – 35746732

Link to DOI – 10.3390/v14061260

Viruses 2022 Jun; 14(6):

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.

https://pubmed.ncbi.nlm.nih.gov/35746732