1. AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.
- Author
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Le, Duc Quang, Nguyen, Son Hoang, Nguyen, Tam Thi, Nguyen, Canh Hao, Ho, Tho Huu, Vo, Nam S., Nguyen, Trang, Nguyen, Hoang Anh, and Cao, Minh Duc
- Subjects
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DRUG resistance in microorganisms , *GENOMICS , *DATA visualization , *DRUG resistance in bacteria , *PAN-genome - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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