{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T06:25:53Z","timestamp":1767853553018,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,11,1]],"date-time":"2019-11-01T00:00:00Z","timestamp":1572566400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100010677","name":"Instituto Nacional de Tecnolog\u00eda Agropecuaria","doi-asserted-by":"publisher","award":["PNSA 1115052"],"award-info":[{"award-number":["PNSA 1115052"]}],"id":[{"id":"10.13039\/501100010677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT 2017-2581"],"award-info":[{"award-number":["PICT 2017-2581"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003074","name":"Agencia Nacional de Promoci\u00f3n Cient\u00edfica y Tecnol\u00f3gica","doi-asserted-by":"publisher","award":["PICT 2014-982"],"award-info":[{"award-number":["PICT 2014-982"]}],"id":[{"id":"10.13039\/501100003074","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.<\/jats:p>","DOI":"10.1093\/bib\/bbz086","type":"journal-article","created":{"date-parts":[[2019,6,25]],"date-time":"2019-06-25T11:18:27Z","timestamp":1561461507000},"page":"1766-1775","source":"Crossref","is-referenced-by-count":10,"title":["A beginner\u2019s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing"],"prefix":"10.1093","volume":"21","author":[{"given":"Marco","family":"Cacciabue","sequence":"first","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABiMo, INTA-CONICET), Hurlingham, Argentina"},{"name":"Departamento de Ciencias B\u00e1sicas, Universidad Nacional de Luj\u00e1n, Luj\u00e1n, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anabella","family":"Curr\u00e1","sequence":"additional","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABiMo, INTA-CONICET), Hurlingham, Argentina"},{"name":"Departamento de Ciencias B\u00e1sicas, Universidad Nacional de Luj\u00e1n, Luj\u00e1n, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elisa","family":"Carrillo","sequence":"additional","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABiMo, INTA-CONICET), Hurlingham, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guido","family":"K\u00f6nig","sequence":"additional","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABiMo, INTA-CONICET), Hurlingham, Argentina"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda In\u00e9s","family":"Gismondi","sequence":"additional","affiliation":[{"name":"Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABiMo, INTA-CONICET), Hurlingham, Argentina"},{"name":"Departamento de Ciencias 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