Search results - 27 results
A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches
still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB Complex (MTBC) member isolates allowing complete characterization including (sub)species ...
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods
bioinformatics workflows and parameters, however, complicates interoperability among (inter)national laboratories. We present a validation strategy applied to a bioinformatics workflow for Illumina data that ...
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 ...
Targeting the 16S rRNA gene for bacterial identification in complex mixed samples: comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies) generation sequencing technologies.
second (Illumina) and third (Oxford Nanopore Technologies (ONT)) generation sequencing technologies for 16S targeted genomics using a well-characterized reference sample. Different 16S gene regions were ...
Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: as a Proof-of-Concept.
and serogroup determination assays, respectively, for both validation datasets. Our WGS workflow has been made publicly available as a “push-button” pipeline for Illumina data at ...
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.
set of 5845 Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362. Using culture based DST as the reference, we estimate to be 100%, 95%, 82%, 99% ...
Complete Genome Sequence of the Lumpy Skin Disease Virus Isolated from the First Reported Case in Greece in 2015
Serafeim C.; Dovas, Chrysostomos I.; Steven Van Borm; Chondrokouki, Eleni D.; Kris De Clercq Source: Genome Announcements, Volume 5, Issue 29 (2017) Keywords: Illumina LSDV Lumpy skin disease NGS WGS Health ...
Use of next‐generation sequencing in microbial risk assessment
Publication Type: Sci. report, recommendat°, guidance doc., directive, monograph Authors: Koenraad Van Hoorde; Francis Butler Source: Volume 16 (2018) Keywords: Food Safety Illumina microbial risk ...
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. ...
Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016.
of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data ...