A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing

Autores
Cacciabue, Marco Polo; Curra, Anabella Paola; Carrillo, Elisa Cristina; Konig, Guido Alberto; Gismondi, Maria Ines
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Instituto de Biotecnología
Fil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Cacciabue, Marco Polo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Cacciabue, Marco Polo. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
Fil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Curra, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Curra, Anabella Paola. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
Fil: Carrillo, Elisa Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Carrillo, Elisa Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Konig, Guido Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Konig, Guido Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Gismondi, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
Fuente
Briefings in Bioinformatics 21 (5) : 1766-1775. (September 2020)
Materia
Genética
Secuencia de ARN
Fiebre Aftosa
Virus Fiebre Aftosa
Genetics
RNA Sequence
Foot and Mouth Disease
Aphthovirus
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/10781
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oai_identifier_str oai:localhost:20.500.12123/10781
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spelling A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencingCacciabue, Marco PoloCurra, Anabella PaolaCarrillo, Elisa CristinaKonig, Guido AlbertoGismondi, Maria InesGenéticaSecuencia de ARNFiebre AftosaVirus Fiebre AftosaGeneticsRNA SequenceFoot and Mouth DiseaseAphthovirusDeep 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.Instituto de BiotecnologíaFil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Cacciabue, Marco Polo. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cacciabue, Marco Polo. Universidad Nacional de Luján. Departamento de Ciencias Básicas; ArgentinaFil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Curra, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Curra, Anabella Paola. Universidad Nacional de Luján. Departamento de Ciencias Básicas; ArgentinaFil: Carrillo, Elisa Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Carrillo, Elisa Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Konig, Guido Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Konig, Guido Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Gismondi, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gismondi, Maria Ines. Universidad Nacional de Luján. Departamento de Ciencias Básicas; ArgentinaOxford Academic Press2021-11-15T17:31:28Z2021-11-15T17:31:28Z2020-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/10781https://academic.oup.com/bib/article/21/5/1766/55650401477-4054https://doi.org/10.1093/bib/bbz086Briefings in Bioinformatics 21 (5) : 1766-1775. (September 2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/PNSA-1115052/AR./Epidemiología y desarrollo de estrategias para la prevención y control de enfermedades que afectan la salud pública, enfermedades exóticas y limitantes del comercio internacional.info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-29T13:45:24Zoai:localhost:20.500.12123/10781instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:45:25.019INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
title A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
spellingShingle A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
Cacciabue, Marco Polo
Genética
Secuencia de ARN
Fiebre Aftosa
Virus Fiebre Aftosa
Genetics
RNA Sequence
Foot and Mouth Disease
Aphthovirus
title_short A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
title_full A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
title_fullStr A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
title_full_unstemmed A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
title_sort A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
dc.creator.none.fl_str_mv Cacciabue, Marco Polo
Curra, Anabella Paola
Carrillo, Elisa Cristina
Konig, Guido Alberto
Gismondi, Maria Ines
author Cacciabue, Marco Polo
author_facet Cacciabue, Marco Polo
Curra, Anabella Paola
Carrillo, Elisa Cristina
Konig, Guido Alberto
Gismondi, Maria Ines
author_role author
author2 Curra, Anabella Paola
Carrillo, Elisa Cristina
Konig, Guido Alberto
Gismondi, Maria Ines
author2_role author
author
author
author
dc.subject.none.fl_str_mv Genética
Secuencia de ARN
Fiebre Aftosa
Virus Fiebre Aftosa
Genetics
RNA Sequence
Foot and Mouth Disease
Aphthovirus
topic Genética
Secuencia de ARN
Fiebre Aftosa
Virus Fiebre Aftosa
Genetics
RNA Sequence
Foot and Mouth Disease
Aphthovirus
dc.description.none.fl_txt_mv 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.
Instituto de Biotecnología
Fil: Cacciabue, Marco Polo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Cacciabue, Marco Polo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Cacciabue, Marco Polo. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
Fil: Curra, Anabella Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Curra, Anabella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Curra, Anabella Paola. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
Fil: Carrillo, Elisa Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Carrillo, Elisa Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Konig, Guido Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Konig, Guido Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Gismondi, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gismondi, Maria Ines. Universidad Nacional de Luján. Departamento de Ciencias Básicas; Argentina
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020-09
2021-11-15T17:31:28Z
2021-11-15T17:31:28Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/10781
https://academic.oup.com/bib/article/21/5/1766/5565040
1477-4054
https://doi.org/10.1093/bib/bbz086
url http://hdl.handle.net/20.500.12123/10781
https://academic.oup.com/bib/article/21/5/1766/5565040
https://doi.org/10.1093/bib/bbz086
identifier_str_mv 1477-4054
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/PNSA-1115052/AR./Epidemiología y desarrollo de estrategias para la prevención y control de enfermedades que afectan la salud pública, enfermedades exóticas y limitantes del comercio internacional.
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford Academic Press
publisher.none.fl_str_mv Oxford Academic Press
dc.source.none.fl_str_mv Briefings in Bioinformatics 21 (5) : 1766-1775. (September 2020)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.559606

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