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Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination.

view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads ...

Use of next‐generation sequencing in microbial risk assessment

assessment MinION MiSeq nanopore sequencing next generation sequencing Abstract: Despite the ever increase in rigorous control and monitoring measures to assure safe food along the entire farm‐to‐fork chain, ...

Complete Genome Sequence of an Avian Metapneumovirus Subtype A Strain Isolated from Chicken () in Brazil.

metapneumovirus (aMPV) isolated from a tracheal tissue sample of a commercial layer flock. The complete genome sequence of aMPV-A/chicken/Brazil- SP /669/2003 was obtained using MiSeq (Illumina, Inc.) sequencing. ...

Development and implementation of a transversal NGS & bioinformatics platform at the Belgian Institute of Public Health

into public health policy. The platform has built up the capacity to both generate and analyze NGS data through an in-house Miseq and advanced bioinformatics pipelines and databases. These services are ...

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.

Nextera XT library preparation; (ii) MiSeq sequencing (data quality, read mapping against plasmid and chromosome references); and (iii) WGS data analysis, i.e. isolate characterization (serotyping, ...

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