Emerging Microbes & Infections · 2022 · 19 citations · 37 references
Life SciencesInfectious DiseasesMicrobiologyHost-pathogen InteractionsMedical MicrobiologyMicrobial PathogenesisBacterial InfectionsBacterial Virulence FactorsPulmonary InfectionsRespiratory InfectionsRespiratory Infectious DiseasesRespiratory Tract InfectionsAntibiotic Resistance In Respiratory PathogensBacterial Virulence GenesComparative Genomics Of PathogensGene Ontology AnalysisPulmonary Clearance MechanismsRespiratory MicrobiologyVirulence Gene AnalysisVirulence Gene Identification
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Prokka: rapid prokaryotic genome annotation
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Roary: rapid large-scale prokaryote pan genome analysis
Andrew J. Page, Carla Cummins, Martin Hunt et al. · Bioinformatics · 2015 · 5.9K citations · Full text
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Michael Inouye, Harriet Dashnow, Lesley-Ann Raven et al. · Genome Medicine · 2014 · 1.1K citations · Full text