ArticleMicroorganisms2022
A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data.
Article in Microorganisms, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Incidence of Streptococcus spp. and whole genome sequencing of Streptococcus agalactiae isolated from cow's milk samples in Brazil.Veterinary research communications · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Genomic insights into Serratia bockelmanii strain 201: unlocking its potential for plant growth promotion and salt stress tolerance.BMC microbiology · 2026Article
- Are the genomes of motileMicrobial genomics · 2026Article
- Inference of antimicrobial resistance (AMR) from a whole genome database outperforming AMR gene detection.iScience · 2025Article
- Genomic diversity and evolutionary patterns ofMicrobial genomics · 2025Article
- Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Klebsiella pneumoniae.BMC microbiology · 2025Article
- Tracing microbial hazards in the aquatic supply chain: challenges, technologies, and future directions.Frontiers in nutrition · 2025Review
- Appelmans protocol - A directed in vitro evolution enables induction and recombination of prophages with expanded host range.Virus research · 2024Article
- First comparative genomics analysis of Corynebacterium auriscanis.Memorias do Instituto Oswaldo Cruz · 2024Article
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- Whole genome sequencing and antimicrobial resistance among clinical isolates of Shigella sonnei in Addis Ababa, Ethiopia.PloS one · 2024Article
- Prevalence ofFoods (Basel, Switzerland) · 2023Article
- Model Organism Modifier (MOM): a user-friendly Galaxy workflow to detect modifiers from genome sequencing data using Caenorhabditis elegans.G3 (Bethesda, Md.) · 2023Article
- Review
- Bacterial Genomics and Epidemiology.Microorganisms · 2023Article
- Non-tuberculous mycobacterial disease associated withFrontiers in veterinary science · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogenetic clustering and sequence typing. Workflow was tested using a collection of 22 in-house sequences of
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