Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example.
J Vis Exp
; (157)2020 03 11.
Article
em En
| MEDLINE
| ID: mdl-32225162
ABSTRACT
Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group of genetically related viruses. In addition to confirmation of the virus presence, sequencing can be used for genomic epidemiology studies, to track viruses and unravel origins, reservoirs and modes of transmission. For such applications, it is crucial to understand possible effects of the error rate associated with the platform used. Routine application in clinical and public health settings require that this is documented with every important change in the protocol. Previously, a protocol for whole genome Usutu virus sequencing on the nanopore sequencing platform was validated (R9.4 flowcell) by direct comparison to Illumina sequencing. Here, we describe the method used to determine the required read coverage, using the comparison between the R10 flow cell and Illumina sequencing as an example.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma Viral
/
Flavivirus
/
Sequenciamento Completo do Genoma
/
Sequenciamento por Nanoporos
Tipo de estudo:
Guideline
Limite:
Humans
Idioma:
En
Revista:
J Vis Exp
Ano de publicação:
2020
Tipo de documento:
Article