AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a...

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Published inBMC bioinformatics Vol. 25; no. 1; p. 193
Main Authors Le, Duc Quang, Nguyen, Son Hoang, Nguyen, Tam Thi, Nguyen, Canh Hao, Ho, Tho Huu, Vo, Nam S, Nguyen, Trang, Nguyen, Hoang Anh, Cao, Minh Duc
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 16.05.2024
BioMed Central
BMC
Subjects
Analysis
Annotations
Anopheles
Anti-Bacterial Agents - pharmacology
Antibiotic resistance
Antibiotics
Antimicrobial resistance
Availability
Bacteria - drug effects
Bacteria - genetics
Best practice
Bioinformatics
Collection management
DNA sequencing
Drug resistance
Drug resistance in microorganisms
Drug Resistance, Bacterial - genetics
Gene clusters
Genes
Genetic aspects
Genome, Bacterial
Genomes
Genomic analysis
Genomics
Genomics - methods
Imipenem
Metadata
Microbial genomics
Nucleotide sequencing
Phylogeny
Proteins
Software
Toolkits
Virulence
Visualization
Vietnam
Visualization
Microbial genomics
Antimicrobial resistance
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Abstract We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .
AbstractList We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz.
Abstract We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .
We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at https://github.com/amromics/amrviz .
We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform comprehensive analysis of a collection of samples directly from raw sequencing data with a single command line. The analysis results in a report showing the genome structure, genome annotations, antibiotic resistance and virulence profile for each sample. The pan-genome of all samples of the collection is analyzed to identify core- and accessory-genes. Phylogenies of the whole genome as well as all gene clusters are also generated. The toolkit provides a web-based visualization dashboard allowing researchers to interactively examine various aspects of the analysis results. Availability: AMRViz is implemented in Python and NodeJS, and is publicly available under open source MIT license at Keywords: Microbial genomics, Visualization, Antimicrobial resistance
ArticleNumber 193
Audience Academic
Author Vo, Nam S
Cao, Minh Duc
Nguyen, Trang
Nguyen, Tam Thi
Ho, Tho Huu
Le, Duc Quang
Nguyen, Hoang Anh
Nguyen, Son Hoang
Nguyen, Canh Hao
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Issue 1
Keywords Visualization
Microbial genomics
Antimicrobial resistance
Language English
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Snippet We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice...
Abstract We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best...
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SubjectTerms Analysis
Annotations
Anopheles
Anti-Bacterial Agents - pharmacology
Antibiotic resistance
Antibiotics
Antimicrobial resistance
Availability
Bacteria - drug effects
Bacteria - genetics
Best practice
Bioinformatics
Collection management
DNA sequencing
Drug resistance
Drug resistance in microorganisms
Drug Resistance, Bacterial - genetics
Gene clusters
Genes
Genetic aspects
Genome, Bacterial
Genomes
Genomic analysis
Genomics
Genomics - methods
Imipenem
Metadata
Microbial genomics
Nucleotide sequencing
Phylogeny
Proteins
Software
Toolkits
Virulence
Visualization
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Title AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
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