Search results - 22 results

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics

collections Cyanobacteria Genomics Gloeobacterales Metagenomics nextflow phylogenomics Phylogeny Singularity containers Workflow Abstract: Background: Microbial culture collections play a key role in taxonomy ...

RNA sequencing of avian paramyxovirus (Paramyxoviridae, Avulavirinae) isolates from wild mallards in Belgium, 2021: complete genomes and coinfections.

genome segments of an AIV of subtype H11N9 could be de novo assembled from the sequencing data. Besides an AIV coinfection, RNA metagenomic data from the APMV-4 isolate also showed evidence of ...

Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillanceAbstract

Publication Type: Peer reviewed scientific article Authors: Bram Bloemen; Mathieu Gand; Kevin Vanneste; Marchal, Kathleen; Nancy Roosens; Sigrid C.J. De Keersmaecker Source: Scientific Reports, Volume 13, Issue 1 (2023) Health Topics:  Health and environm ...

Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products

12, Issue 12 (2022) Keywords: Bacillus food enzyme genetically modified microorganisms (GMM) hybrid genome assembly metagenomic shotgun sequencing Abstract: Genetically modified microorganisms (GMM) are ...

Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study

Publication Type: Peer reviewed scientific article Authors: Florence E Buytaers; Bavo Verhaegen; Mathieu Gand; Jolien D'aes; Kevin Vanneste; Nancy Roosens; Kathleen Marchal; Sarah Denayer; Sigrid C.J. De Keersmaecker Source: Foods, Volume 11, Issue 2 ...

Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing

of interest into raw wild-type sequencing data, or by mixing wild-type and mutant raw sequencing data, to construct mixed samples subjected to WGS using a tiling amplicon-based targeted metagenomics ...

Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.

identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical ...

Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak

Pochet, Brigitte; Vera Cantaert; Marchal, Kathleen; Sarah Denayer; Sigrid C.J. De Keersmaecker Source: Microbial Genomics, Volume 7, Issue 4 (2021) Keywords: food surveillance Metagenomics outbreak ...

Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies

Sigrid C.J. De Keersmaecker Source: Frontiers in Microbiology, Volume 12 (2021) Keywords: Flongle food surveillance Metagenomics nanopore outbreak SNP analysis STEC strain-level Abstract: The current ...

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