AMRViz

AMRViz analyzes, visualizes, and manages bacterial genomics samples through a best-practice analysis pipeline that processes raw sequencing data to generate genome structure, annotations, antimicrobial resistance profiles, virulence profiles, pan-genome analyses, and phylogenies.

Key Features:

• Comprehensive Genome Analysis: Processes raw sequencing data to generate genome structure and genome annotations for each sample.
• Antimicrobial Resistance Profiling: Identifies antibiotic resistance profiles for individual bacterial samples.
• Virulence Profiling: Determines virulence profiles for each analyzed sample.
• Pan-Genome Analysis: Analyzes the pan-genome of all samples in a collection to identify core and accessory genes.
• Phylogenetic Analysis: Generates phylogenies of the whole genome and all gene clusters.

Scientific Applications:

• Antimicrobial Resistance Surveillance: Enables comprehensive analysis and visualization of antimicrobial resistance in bacterial collections.
• Bacterial Population Genomics: Supports pan-genome and phylogenetic studies to understand gene content variation and evolutionary relationships across bacterial samples.
• Virulence Characterization: Facilitates identification of virulence determinants in bacterial pathogens.

Methodology:

AMRViz implements a best-practice analysis pipeline executed via a single command line, implemented in Python and NodeJS.