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Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.<\/jats:p>","DOI":"10.3390\/v15020587","type":"journal-article","created":{"date-parts":[[2023,2,21]],"date-time":"2023-02-21T02:30:35Z","timestamp":1676946635000},"page":"587","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3428-2168","authenticated-orcid":false,"given":"Marta","family":"Iba\u00f1ez-Lligo\u00f1a","sequence":"first","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain"},{"name":"Biochemistry and Molecular Biology Department, Universitat Aut\u00f2noma de Barcelona (UAB), Campus de la UAB, Pla\u00e7a C\u00edvica, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergi","family":"Colomer-Castell","sequence":"additional","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain"},{"name":"Biochemistry and Molecular Biology Department, Universitat Aut\u00f2noma de Barcelona (UAB), Campus de la UAB, Pla\u00e7a C\u00edvica, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandra","family":"Gonz\u00e1lez-S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Microbiology Department, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4253-8015","authenticated-orcid":false,"given":"Josep","family":"Gregori","sequence":"additional","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Campos","sequence":"additional","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. 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Monforte de Lemos, 3-5, 28029 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Andr\u00e9s","sequence":"additional","affiliation":[{"name":"Microbiology Department, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Pi\u00f1ana","sequence":"additional","affiliation":[{"name":"Microbiology Department, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom\u00e0s","family":"Pumarola","sequence":"additional","affiliation":[{"name":"Microbiology Department, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Microbiology Department, Universitat Aut\u00f2noma de Barcelona (UAB), Campus de la UAB, Pla\u00e7a C\u00edvica, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9128-7013","authenticated-orcid":false,"given":"Francisco","family":"Rodr\u00edguez-Frias","sequence":"additional","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain"},{"name":"Department of Basic Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vall\u00e8s, 08195 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"Ant\u00f3n","sequence":"additional","affiliation":[{"name":"Microbiology Department, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Microbiology Department, Universitat Aut\u00f2noma de Barcelona (UAB), Campus de la UAB, Pla\u00e7a C\u00edvica, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0014-084X","authenticated-orcid":false,"given":"Josep","family":"Quer","sequence":"additional","affiliation":[{"name":"Liver Diseases-Viral Hepatitis, Liver Unit, Vall d\u2019Hebron Institut de Recerca (VHIR), Vall d\u2019Hebron Hospital Universitari, Vall d\u2019Hebron Barcelona Hospital Campus, Passeig Vall d\u2019Hebron 119-129, 08035 Barcelona, Spain"},{"name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Hep\u00e1ticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain"},{"name":"Biochemistry and Molecular Biology Department, Universitat Aut\u00f2noma de Barcelona (UAB), Campus de la UAB, Pla\u00e7a C\u00edvica, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/nrmicro2147","article-title":"Coronaviruses post-SARS: Update on replication and pathogenesis","volume":"7","author":"Perlman","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","unstructured":"Domingo, E. (1994). Mutation Rates and Rapid Evolution of RNA Viruses. Evol. Biol. 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