A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
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 affor...
| Main Authors: | , , , , |
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| Format: | Artículo |
| Language: | Inglés |
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Oxford Academic Press
2021
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| Online Access: | 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 |
| _version_ | 1855484654919876608 |
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| author | Cacciabue, Marco Polo Curra, Anabella Paola Carrillo, Elisa Cristina Konig, Guido Alberto Gismondi, Maria Ines |
| author_browse | Cacciabue, Marco Polo Carrillo, Elisa Cristina Curra, Anabella Paola Gismondi, Maria Ines Konig, Guido Alberto |
| author_facet | Cacciabue, Marco Polo Curra, Anabella Paola Carrillo, Elisa Cristina Konig, Guido Alberto Gismondi, Maria Ines |
| author_sort | Cacciabue, Marco Polo |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA10781 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford Academic Press |
| publisherStr | Oxford Academic Press |
| record_format | dspace |
| spelling | INTA107812021-11-15T17:33:58Z A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing Cacciabue, Marco Polo Curra, Anabella Paola Carrillo, Elisa Cristina Konig, Guido Alberto Gismondi, Maria Ines Genética Secuencia de ARN Fiebre Aftosa Virus Fiebre Aftosa Genetics RNA Sequence Foot and Mouth Disease Aphthovirus 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 2021-11-15T17:31:28Z 2021-11-15T17:31:28Z 2020-09 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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. 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) application/pdf Oxford Academic Press Briefings in Bioinformatics 21 (5) : 1766-1775. (September 2020) |
| spellingShingle | Genética Secuencia de ARN Fiebre Aftosa Virus Fiebre Aftosa Genetics RNA Sequence Foot and Mouth Disease Aphthovirus Cacciabue, Marco Polo Curra, Anabella Paola Carrillo, Elisa Cristina Konig, Guido Alberto Gismondi, Maria Ines 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 |
| 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_short | A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing |
| title_sort | beginner s guide for fmdv quasispecies analysis sub consensus variant detection and haplotype reconstruction using next generation sequencing |
| topic | Genética Secuencia de ARN Fiebre Aftosa Virus Fiebre Aftosa Genetics RNA Sequence Foot and Mouth Disease Aphthovirus |
| 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 |
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