Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples
Abstract New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-08-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | https://doi.org/10.1186/s43141-023-00536-3 |
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| author | Leandro Menezes de Souza Isabelle Dias de Oliveira Flávia Cristina Silva Sales Antonio Charlys da Costa Karoline Rodrigues Campos Adriano Abbud Juliana Mariotti Guerra Cinthya dos Santos Cirqueira Borges Carlos Pires Fernandes Júnior Takahashi Leonardo José Tadeu de Araújo |
| author_facet | Leandro Menezes de Souza Isabelle Dias de Oliveira Flávia Cristina Silva Sales Antonio Charlys da Costa Karoline Rodrigues Campos Adriano Abbud Juliana Mariotti Guerra Cinthya dos Santos Cirqueira Borges Carlos Pires Fernandes Júnior Takahashi Leonardo José Tadeu de Araújo |
| author_sort | Leandro Menezes de Souza |
| collection | DOAJ |
| description | Abstract New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype. |
| first_indexed | 2024-03-12T04:04:58Z |
| format | Article |
| id | doaj.art-b71fdac24a2c4edaa62d7e77a1e0d6a2 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2025-03-22T04:37:41Z |
| publishDate | 2023-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-b71fdac24a2c4edaa62d7e77a1e0d6a22024-04-28T00:25:55ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202023-08-012111810.1186/s43141-023-00536-3Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samplesLeandro Menezes de Souza0Isabelle Dias de Oliveira1Flávia Cristina Silva Sales2Antonio Charlys da Costa3Karoline Rodrigues Campos4Adriano Abbud5Juliana Mariotti Guerra6Cinthya dos Santos Cirqueira Borges7Carlos Pires Fernandes Júnior Takahashi8Leonardo José Tadeu de Araújo9 Centro de Patologia, Instituto Adolfo Lutz Centro de Patologia, Instituto Adolfo LutzDepartamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São PauloDepartamento de Moléstias Infecciosas e Parasitárias, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo Centro de Respostas Rápidas, Instituto Adolfo Lutz Centro de Respostas Rápidas, Instituto Adolfo Lutz Centro de Patologia, Instituto Adolfo Lutz Centro de Patologia, Instituto Adolfo LutzState Health Secretary of São Paulo Centro de Patologia, Instituto Adolfo LutzAbstract New-generation sequencing (NGS) techniques have brought the opportunity for genomic monitoring of several microorganisms potentially relevant to public health. The establishment of different methods with different mechanisms provides a wide choice, taking into account several aspects. With that in mind, the present aim of the study was to compare basic genomic sequencing metrics that could potentially impact genotyping by nanopores from Oxford Nanopore Technologies and by synthesis from Illumina in clinical samples positive for Chikungunya (CHIKV). Among the metrics studied, running time, read production, and Q score were better represented in Illumina sequencing, while the MinIOn platform showed better response time and greater diversity of generated files. That said, it was possible to establish differences between the studied metrics in addition to verifying that the distinctions in the methods did not impact the identification of the CHIKV virus genotype.https://doi.org/10.1186/s43141-023-00536-3Next-generation sequencingMetric MinION and IlluminaChikungunya virus genotype |
| spellingShingle | Leandro Menezes de Souza Isabelle Dias de Oliveira Flávia Cristina Silva Sales Antonio Charlys da Costa Karoline Rodrigues Campos Adriano Abbud Juliana Mariotti Guerra Cinthya dos Santos Cirqueira Borges Carlos Pires Fernandes Júnior Takahashi Leonardo José Tadeu de Araújo Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples Journal of Genetic Engineering and Biotechnology Next-generation sequencing Metric MinION and Illumina Chikungunya virus genotype |
| title | Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples |
| title_full | Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples |
| title_fullStr | Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples |
| title_full_unstemmed | Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples |
| title_short | Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples |
| title_sort | technical comparison of minion and illumina technologies for genotyping chikungunya virus in clinical samples |
| topic | Next-generation sequencing Metric MinION and Illumina Chikungunya virus genotype |
| url | https://doi.org/10.1186/s43141-023-00536-3 |
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