{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:17:06Z","timestamp":1790759826435,"version":"4.1.0"},"reference-count":62,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,10]],"date-time":"2022-06-10T00:00:00Z","timestamp":1654819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004663","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}],"id":[{"id":"10.13039\/501100004663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Alliance of International Scientific Organizations","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}]},{"name":"Alliance of International Scientific Organizations","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}]},{"name":"Alliance of International Scientific Organizations","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}]},{"name":"Institut Pasteur","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}]},{"name":"Institut Pasteur","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}]},{"name":"Institut Pasteur","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}]},{"name":"Fondation Merieux","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}]},{"name":"Fondation Merieux","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}]},{"name":"Fondation Merieux","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}]},{"name":"Chinese Academy of Sciences","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}]},{"name":"Chinese Academy of Sciences","award":["ANSO-CR-SP-2020-02"],"award-info":[{"award-number":["ANSO-CR-SP-2020-02"]}]},{"name":"Chinese Academy of Sciences","award":["2019SHZDZX02"],"award-info":[{"award-number":["2019SHZDZX02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/v14061260","type":"journal-article","created":{"date-parts":[[2022,6,13]],"date-time":"2022-06-13T06:31:59Z","timestamp":1655101919000},"page":"1260","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data"],"prefix":"10.3390","volume":"14","author":[{"given":"Emilio","family":"Mastriani","sequence":"first","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathrina Mae","family":"Bienes","sequence":"additional","affiliation":[{"name":"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"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary","family":"Wong","sequence":"additional","affiliation":[{"name":"Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Berthet","sequence":"additional","affiliation":[{"name":"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"},{"name":"Unit\u00e9 Environnement et Risque Infectieux, Institut Pasteur, Cellule d\u2019Intervention Biologique d\u2019Urgence, 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1128\/JCM.01967-16","article-title":"Integrating Advanced Molecular Technologies into Public Health","volume":"55","author":"Gwinn","year":"2017","journal-title":"J. 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