ASA3P

ASA3P automates the processing, assembly, annotation, and genome-wide analysis of bacterial whole-genome sequencing data to produce standardized assemblies and characterize taxonomic identity, antibiotic resistance genes, and virulence factors.

Key Features:

• Automatic data processing: Automates preprocessing including quality clipping of raw sequencing reads and assembly into contigs.
• Scaffolding: Arranges contigs into larger genomic structures to provide context for annotation.
• Annotation: Identifies genes and other functional elements within assembled genomes.
• Taxonomic classification: Performs taxonomic assignment of bacterial genomes.
• Antibiotic resistance gene detection: Detects antibiotic resistance genes to support antimicrobial resistance studies.
• Virulence factor identification: Identifies virulence factors contributing to pathogenicity.
• Scalable architecture: Supports local Docker container deployment and an OpenStack-based cloud version with dynamic self-scaling compute clusters for projects of varying scale.
• Standard output formats: Provides intermediate and final results in standard bioinformatics file formats.

Scientific Applications:

• Microbiology: Standardized processing and comparative analysis of bacterial whole genomes.
• Epidemiology: Surveillance and outbreak investigations through taxonomic classification and resistance profiling.
• Infectious disease research: Characterization of virulence factors and antimicrobial resistance mechanisms.
• Comparative genomics and evolution: High-throughput analyses to study bacterial evolution, pathogenesis, and resistance mechanisms.

Methodology:

Quality clipping of reads, assembly into contigs, scaffolding of contigs, genome annotation, and genome-wide characterizations including taxonomic classification, antibiotic resistance gene detection, and virulence factor identification.