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In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A\/B), as well as a \u201cgeneric\u201d build for other viruses); and (v)\n                      <jats:italic>algn2pheno<\/jats:italic>\n                      for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with\/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed\n                      <jats:italic>findONTime<\/jats:italic>\n                      , a tool aimed at reducing costs and the time between sample reception and diagnosis.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/insaflu.insa.pt\/\">https:\/\/insaflu.insa.pt\/<\/jats:ext-link>\n                      (online tool) and\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/INSaFLU\">https:\/\/github.com\/INSaFLU<\/jats:ext-link>\n                      (code).\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13073-024-01334-3","type":"journal-article","created":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T19:02:34Z","timestamp":1713985354000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance"],"prefix":"10.1186","volume":"16","author":[{"given":"Jo\u00e3o Dourado","family":"Santos","sequence":"first","affiliation":[]},{"given":"Daniel","family":"Sobral","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Pinheiro","sequence":"additional","affiliation":[]},{"given":"Joana","family":"Isidro","sequence":"additional","affiliation":[]},{"given":"Carlijn","family":"Bogaardt","sequence":"additional","affiliation":[]},{"given":"Miguel","family":"Pinto","sequence":"additional","affiliation":[]},{"given":"Rodrigo","family":"Eus\u00e9bio","sequence":"additional","affiliation":[]},{"given":"Andr\u00e9","family":"Santos","sequence":"additional","affiliation":[]},{"given":"Rafael","family":"Mamede","sequence":"additional","affiliation":[]},{"given":"Daniel L.","family":"Horton","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o Paulo","family":"Gomes","sequence":"additional","affiliation":[]},{"name":"TELEVIR Consortium","sequence":"additional","affiliation":[]},{"given":"Laurent","family":"Bigarr\u00e9","sequence":"additional","affiliation":[]},{"given":"Jovita","family":"Fern\u00e1ndez-Pinero","sequence":"additional","affiliation":[]},{"given":"Ricardo J.","family":"Pais","sequence":"additional","affiliation":[]},{"given":"Maurilia","family":"Marcacci","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Moreno","sequence":"additional","affiliation":[]},{"given":"Tobias","family":"Lilja","sequence":"additional","affiliation":[]},{"given":"\u00d8ivind","family":"\u00d8ines","sequence":"additional","affiliation":[]},{"given":"Artur","family":"Rze\u017cutka","sequence":"additional","affiliation":[]},{"given":"Elisabeth","family":"Mathijs","sequence":"additional","affiliation":[]},{"given":"Steven","family":"Van Borm","sequence":"additional","affiliation":[]},{"given":"Morten","family":"Rasmussen","sequence":"additional","affiliation":[]},{"given":"Katja","family":"Spiess","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3767-2209","authenticated-orcid":false,"given":"V\u00edtor","family":"Borges","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,4,25]]},"reference":[{"key":"1334_CR1","doi-asserted-by":"publisher","first-page":"20386","DOI":"10.2807\/ese.18.04.20386-en","volume":"18","author":"MJ Struelens","year":"2013","unstructured":"Struelens MJ, Brisse S. 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