start-asap

start-asap implements the ASA3P automated and scalable pipeline for bacterial whole-genome sequencing (WGS) analysis, performing quality clipping, assembly, scaffolding, annotation, taxonomic classification, antibiotic resistance gene detection, and virulence factor identification.

Key Features:

• Automated Workflow: Automates processing from raw sequencing reads through quality clipping, assembly into contigs, scaffolding, and genome annotation.
• Comprehensive Characterization: Performs taxonomic classification, detection of antibiotic resistance genes, and identification of virulence factors.
• Standardized Outputs: Produces intermediate and final results in standard bioinformatics file formats for downstream analysis.
• Scalability and Deployment Options: Provides a Docker container for small-to-medium projects and an OpenStack-based cloud version that supports automatic creation and management of self-scaling compute clusters for large-scale analyses.
• Standardization: Enforces a standardized pipeline to ensure consistency across comparative genomics and meta-analyses.

Scientific Applications:

• Taxonomic classification: Assigns bacterial species and taxonomic ranks from WGS data.
• Antibiotic resistance surveillance: Identifies and characterizes antibiotic resistance genes from assembled genomes.
• Virulence factor analysis: Detects and annotates virulence factors relevant to pathogenicity studies.
• Large-scale bacterial genomics: Enables rapid, standardized analysis of hundreds of bacterial genomes for comparative and epidemiological studies.

Methodology:

Computational steps explicitly include quality clipping of reads, assembly into contigs, scaffolding, genome annotation, taxonomic classification, detection of antibiotic resistance genes, identification of virulence factors, and optional deployment on Docker or OpenStack with automatic self-scaling compute cluster management.