Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples.
Chikungunya virus genotype
Metric MinION and Illumina
Next-generation sequencing
Journal
Journal, genetic engineering & biotechnology
ISSN: 2090-5920
Titre abrégé: J Genet Eng Biotechnol
Pays: Netherlands
ID NLM: 101317150
Informations de publication
Date de publication:
29 Aug 2023
29 Aug 2023
Historique:
received:
16
12
2022
accepted:
27
07
2023
medline:
29
8
2023
pubmed:
29
8
2023
entrez:
29
8
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37642827
doi: 10.1186/s43141-023-00536-3
pii: 10.1186/s43141-023-00536-3
pmc: PMC10465416
doi:
Types de publication
Journal Article
Langues
eng
Pagination
88Subventions
Organisme : FESIMA
ID : CAF 042/2021 (SES-OFI-2021/29090).
Informations de copyright
© 2023. Academy of Scientific Research and Technology.
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